PrecisionFDA
Hidden Treasures - Warm Up
Find variants injected into an NGS dataset
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Starts
2017-07-18 00:00:00 UTC
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Ends
2017-09-13 06:59:00 UTC
At the start of this challenge, users were provided with a NA12878 whole exome sequencing FASTQ file that had been in silico modified with single nucleotide variants (SNVs) and insertion and deletion (InDel) variants (less than 40 bp) at approximate Variant Allele Frequencies (VAFs) ≥20%. This precisionFDA note summarizes certain precisionFDA artifacts related to the challenge, including a VCF with the injected variants, as well as the VCF evaluation app which was used by the system to automatically evaluate all entries. We invite the community to try the evaluation app and give us any feedback.
Challenge participants ran the modified FASTQ file through their pipeline(s), and returned the resulting VCF file to precisionFDA for comparison to the known reference truth using a VCF evaluation app that we created. The first table below shows calls for 50 injected variants, including SNVs and InDels sorted separately by size (1-3 bp, 4-6 bp, 7-9 bp, 10-12 bp, and larger than 13 bp), for each entry in a separate row. Results shown for each entry also include whole exome recall, precision and F-score* for overall SNVs and overall InDels:
- Recall, or sensitivity, reflects the percentage of variants in the NIST/GiaB benchmark set that were exactly called by the challenge participant pipeline in a submitted dataset.
- Precision, or positive predictive value, reflects the percentage of called variants which match exactly the NIST/GiaB benchmark set.
- F-score is the harmonic mean of recall and precision, and is sometimes used as a single combined metric for evaluating overall accuracy.
Participants whose submissions correctly detected and called all 50 injected variants (regardless of the whole exome precision, recall and F-score for their pipeline/submission) are being recognized as Warm Up in silico Variant Catchers and are designated with the Variant Catcher icon in the table (45 entries earned that title).
* The terminology currently used in this discussion (such as "precision" and "recall") is not necessarily harmonized with definitions used by ISO, CLSI, or FDA, but are terms commonly used by NGS software developers.
Injected indels | Injected | Whole-exome SNP | Whole-exome indel | ||||||||||||
Submitter | Organization | Entry | 1-3 | 4-6 | 7-9 | 10-12 | 13+ | SNPS | Total | precision | recall | F-score | precision | recall | F-score |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Vijay Walia Variant Catcher | FDA | VW_submission_1 | 11 | 11 | 11 | 11 | 1 | 5 | 50 | 0.990646 | 0.99029 | 0.990468 | 0.716542 | 0.858191 | 0.780996 |
Justin Lack Variant Catcher | NIH | JLack_CCBR_Leidos_StandardPipeline_relaxed | 11 | 11 | 11 | 11 | 1 | 5 | 50 | 0.993357 | 0.988074 | 0.990708 | 0.788118 | 0.858511 | 0.82181 |
Justin Lack Variant Catcher | NIH | JLack_CCBR_Leidos_StandardPipeline_noFilter | 11 | 11 | 11 | 11 | 1 | 5 | 50 | 0.990352 | 0.988212 | 0.989281 | 0.710399 | 0.860213 | 0.778161 |
Chung Tsai Su | Atgenomix | SeqsLab with GATK-based Parallelization | 11 | 11 | 11 | 11 | 0 | 5 | 49 | 0.994188 | 0.976203 | 0.985113 | 0.695819 | 0.849043 | 0.764832 |
Chung Tsai Su | Atgenomix | SeqsLab with GATK-based Parallelization(conf>30) | 11 | 11 | 11 | 11 | 0 | 5 | 49 | 0.995428 | 0.974222 | 0.984711 | 0.746753 | 0.843404 | 0.792141 |
Igor Dolgalev Variant Catcher | NYU Langone Medical Center | GATK HaplotypeCaller unfiltered | 11 | 11 | 11 | 11 | 1 | 5 | 50 | 0.985822 | 0.982145 | 0.98398 | 0.751669 | 0.854043 | 0.799592 |
Igor Dolgalev Variant Catcher | NYU Langone Medical Center | GATK HaplotypeCaller depth-filtered | 11 | 11 | 11 | 11 | 1 | 5 | 50 | 0.986218 | 0.903786 | 0.943204 | 0.743792 | 0.792979 | 0.767598 |
Theresa Wohlever Variant Catcher | Test | 11 | 11 | 11 | 11 | 1 | 5 | 50 | 0.991177 | 0.991343 | 0.99126 | 0.661186 | 0.867447 | 0.750401 | |
Rafael Aldana Variant Catcher | Sentieon Inc | Sentieon_DNAseq_std-NA12878MOD | 11 | 11 | 11 | 11 | 1 | 5 | 50 | 0.995136 | 0.989085 | 0.992101 | 0.748639 | 0.86266 | 0.801615 |
Rafael Aldana Variant Catcher | Sentieon Inc | Sentieon_TNscope_Tonly_std-NA12878MOD | 11 | 11 | 11 | 11 | 1 | 5 | 50 | 0.600924 | 0.598465 | 0.599692 | 0.394585 | 0.413936 | 0.404029 |
Jongsuk Chung | Samsung Genome Institute | SGI_1st_result | 4 | 6 | 6 | 4 | 0 | 4 | 24 | 0.990799 | 0.989002 | 0.9899 | 0.752093 | 0.859362 | 0.802157 |
Jongsuk Chung | Samsung Genome Institute | SGI_2nd_filtration | 5 | 9 | 7 | 7 | 0 | 5 | 33 | 0.9893 | 0.991357 | 0.990327 | 0.697161 | 0.866489 | 0.772657 |
Jongsuk Chung | Samsung Genome Institute | SGI_4th_filtration | 7 | 11 | 8 | 10 | 1 | 5 | 42 | 0.587313 | 0.601263 | 0.594206 | 0.432052 | 0.43734 | 0.43468 |
Jongsuk Chung | Samsung Genome Institute | SGI_3rd_filtration_rere | 7 | 10 | 6 | 8 | 0 | 5 | 36 | 0.964913 | 0.991744 | 0.978145 | 0.612791 | 0.843085 | 0.709724 |
Mark Cowley Variant Catcher | Garvan Institute | KCCG_1.7.0_HC | 11 | 11 | 11 | 11 | 1 | 5 | 50 | 0.995136 | 0.989085 | 0.992101 | 0.727712 | 0.865 | 0.790439 |
Mark Cowley | Garvan Institute | KCCG_1.7.0_VD | 11 | 10 | 9 | 11 | 1 | 5 | 47 | 0.996376 | 0.96972 | 0.982867 | 0.805216 | 0.745665 | 0.774297 |
Rongshan Yu Variant Catcher | Aginome Scientific | NA12878MOD.imp.vcf.gz | 11 | 11 | 11 | 11 | 1 | 5 | 50 | 0.992302 | 0.990955 | 0.991628 | 0.701692 | 0.859681 | 0.772693 |
Rafael Aldana Variant Catcher | Sentieon Inc | Sentieon_DNAseq_nodecoy-NA12878MOD | 11 | 11 | 11 | 11 | 1 | 5 | 50 | 0.991941 | 0.988905 | 0.99042 | 0.751527 | 0.862872 | 0.80336 |
Rafael Aldana Variant Catcher | Sentieon Inc | Sentieon_TNscope_Tonly_nodecoy-NA12878MOD | 11 | 11 | 11 | 11 | 1 | 5 | 50 | 0.598495 | 0.598202 | 0.598348 | 0.39834 | 0.41734 | 0.407619 |
Severine Catreux Variant Catcher | Edico Genome | DRAGEN_DNASeq_NA12878MOD_submission1 | 11 | 11 | 11 | 11 | 1 | 5 | 50 | 0.991705 | 0.991966 | 0.991835 | 0.834423 | 0.895638 | 0.863947 |
Severine Catreux Variant Catcher | Edico Genome | DRAGEN_DNASeq_NA12878MOD_submission2 | 11 | 11 | 11 | 11 | 1 | 5 | 50 | 0.972662 | 0.992271 | 0.982369 | 0.705784 | 0.89917 | 0.790826 |
Severine Catreux | Edico Genome | DRAGEN_DNASeq_NA12878MOD_submission3 | 10 | 11 | 11 | 11 | 1 | 5 | 49 | 0.996531 | 0.990886 | 0.9937 | 0.933809 | 0.820213 | 0.873333 |
Severine Catreux | Edico Genome | DRAGEN_DNASeq_NA12878MOD_submission4 | 10 | 11 | 11 | 11 | 1 | 5 | 49 | 0.998621 | 0.962947 | 0.98046 | 0.957514 | 0.771277 | 0.854364 |
Severine Catreux Variant Catcher | Edico Genome | DRAGEN_DNASeq_NA12878MOD_submission5 | 11 | 11 | 11 | 11 | 1 | 5 | 50 | 0.996848 | 0.990165 | 0.993496 | 0.888806 | 0.883617 | 0.886204 |
Rongshan Yu Variant Catcher | Aginome Scientific | NA12878MOD.imp.v2.recode.vcf.gz | 11 | 11 | 11 | 11 | 1 | 5 | 50 | 0.991168 | 0.991814 | 0.991491 | 0.68785 | 0.861596 | 0.764981 |
Rongshan Yu Variant Catcher | Aginome Scientific | NA12878MOD.imp.v3.recode.vcf | 11 | 11 | 11 | 11 | 1 | 5 | 50 | 0.990116 | 0.992146 | 0.99113 | 0.670604 | 0.862872 | 0.754685 |
Sunho Lee | Syntekabio | ADIscan_NA12878MOD_all | 11 | 11 | 11 | 10 | 0 | 5 | 48 | 0.987261 | 0.989348 | 0.988303 | 0.672161 | 0.82174 | 0.739462 |
Sunho Lee | Syntekabio | ADIscan_NA12878MOD_filtered | 11 | 11 | 11 | 10 | 0 | 5 | 48 | 0.989856 | 0.989029 | 0.989442 | 0.688306 | 0.819506 | 0.748198 |
Sunho Lee | Syntekabio | ADIscan_NA12878MOD_tight | 11 | 11 | 11 | 10 | 0 | 5 | 48 | 0.991681 | 0.988655 | 0.990166 | 0.69806 | 0.817167 | 0.752932 |
Sunho Lee | Syntekabio | ADIscan_NA12878MOD_conf | 11 | 11 | 11 | 10 | 0 | 5 | 48 | 0.99274 | 0.988309 | 0.99052 | 0.70274 | 0.815146 | 0.754781 |
Hua Chen Variant Catcher | Beijing Institute of Genomics | 11 | 11 | 11 | 11 | 1 | 5 | 50 | 0.988619 | 0.988642 | 0.98863 | 0.669671 | 0.823974 | 0.738852 | |
Hua Chen Variant Catcher | BIG_NGSToolkit-NA12878.vcf | 11 | 11 | 11 | 11 | 1 | 5 | 50 | 0.991675 | 0.98842 | 0.990045 | 0.826387 | 0.699574 | 0.757712 | |
Hua Chen Variant Catcher | BIG_CelerSNP-NA12878MOD.vcf | 11 | 11 | 11 | 11 | 1 | 5 | 50 | 0.988619 | 0.988642 | 0.98863 | 0.669671 | 0.823974 | 0.738852 | |
Hua Chen Variant Catcher | BIG_CelerSNP-NA12878.vcf | 11 | 11 | 11 | 11 | 1 | 5 | 50 | 0.988619 | 0.988642 | 0.98863 | 0.669671 | 0.823974 | 0.738852 | |
Liu Xueying | Challenge_submission_20170912_3 | 11 | 11 | 11 | 11 | 0 | 5 | 49 | 0.993592 | 0.249152 | 0.398401 | 0.873303 | 0.041064 | 0.078439 | |
Angela Pozo | INGEMM | HULP-germ | 11 | 11 | 11 | 10 | 0 | 5 | 48 | 0.984124 | 0.325406 | 0.489091 | 0.651468 | 0.132128 | 0.219697 |
Sam Friedman | Broad Institute | Experimental Unfiltered | 11 | 11 | 10 | 11 | 1 | 5 | 49 | 0.993729 | 0.990027 | 0.991874 | 0.68276 | 0.839911 | 0.753226 |
Colin Hercus | Novocraft Technologies | NovoalignFreebayes_1 | 11 | 10 | 10 | 10 | 1 | 5 | 47 | 0.980632 | 0.992949 | 0.986753 | 0.784889 | 0.86263 | 0.821925 |
Colin Hercus | Novocraft Technologies | NovoalignFreebayes_2 | 11 | 10 | 8 | 8 | 1 | 5 | 43 | 0.992934 | 0.992188 | 0.992561 | 0.836097 | 0.839115 | 0.837603 |
Colin Hercus Variant Catcher | Novocraft Technologies | NovoalignGATKHC_1 | 11 | 11 | 11 | 11 | 1 | 5 | 50 | 0.98731 | 0.990512 | 0.988908 | 0.704128 | 0.862872 | 0.775459 |
Shawn Williams | test2 | 6 | 11 | 11 | 11 | 1 | 5 | 45 | 0.264135 | 0.008671 | 0.016791 | 0.192833 | 0.012021 | 0.022632 | |
Colin Hercus Variant Catcher | Novocraft Technologies | NovoalignGATKHC_2 | 11 | 11 | 11 | 11 | 1 | 5 | 50 | 0.98761 | 0.990484 | 0.989045 | 0.705217 | 0.861809 | 0.775689 |
Angela Pozo | INGEMM | HULP-mosaic | 10 | 9 | 6 | 7 | 0 | 3 | 35 | 0.94938 | 0.327677 | 0.487199 | 0.765668 | 0.117447 | 0.203655 |
Tian Xia | Submission1 | 11 | 11 | 11 | 10 | 1 | 5 | 49 | 0.994498 | 0.986481 | 0.990473 | 0.747691 | 0.860532 | 0.800153 | |
Steve Laurie Variant Catcher | CNAG | B8GATK36 | 11 | 11 | 11 | 11 | 1 | 5 | 50 | 0.995892 | 0.973848 | 0.984746 | 0.730212 | 0.835426 | 0.779283 |
Steve Laurie Variant Catcher | CNAG | B15GATK36 | 11 | 11 | 11 | 11 | 1 | 5 | 50 | 0.99592 | 0.973862 | 0.984767 | 0.731095 | 0.835426 | 0.779786 |
Steve Laurie Variant Catcher | CNAG | G3GATK36 | 11 | 11 | 11 | 11 | 1 | 5 | 50 | 0.997145 | 0.972587 | 0.984713 | 0.735245 | 0.834149 | 0.78158 |
Shawn Williams | test | 6 | 11 | 11 | 11 | 1 | 5 | 45 | 0.264135 | 0.008671 | 0.016791 | 0.192833 | 0.012021 | 0.022632 | |
Shawn Williams | test | 6 | 11 | 11 | 11 | 1 | 5 | 45 | 0.264135 | 0.008671 | 0.016791 | 0.192833 | 0.012021 | 0.022632 | |
Charles Chapple Variant Catcher | Saphetor | Saphetor1 | 11 | 11 | 11 | 11 | 1 | 5 | 50 | 0.994249 | 0.960121 | 0.976887 | 0.78657 | 0.830106 | 0.807752 |
Charles Chapple Variant Catcher | Saphetor | Saphetor2 | 11 | 11 | 11 | 11 | 1 | 5 | 50 | 0.993583 | 0.971341 | 0.982336 | 0.818341 | 0.821596 | 0.819965 |
Charles Chapple Variant Catcher | Saphetor | Saphetor4 | 11 | 11 | 11 | 11 | 1 | 5 | 50 | 0.9955 | 0.971133 | 0.983165 | 0.812949 | 0.820745 | 0.816828 |
Charles Chapple Variant Catcher | Saphetor | dummy | 11 | 11 | 11 | 11 | 1 | 5 | 50 | 0.993583 | 0.971341 | 0.982336 | 0.818341 | 0.821596 | 0.819965 |
Shawn Williams Variant Catcher | submission | 11 | 11 | 11 | 11 | 1 | 5 | 50 | 0.978296 | 0.986536 | 0.982399 | 0.694895 | 0.860851 | 0.769021 | |
Zitong He Variant Catcher | MySubmission1 | 11 | 11 | 11 | 11 | 1 | 5 | 50 | 0.978296 | 0.986536 | 0.982399 | 0.694895 | 0.860851 | 0.769021 | |
Charles Chapple Variant Catcher | Saphetor | dummy | 11 | 11 | 11 | 11 | 1 | 5 | 50 | 0.980753 | 0.983655 | 0.982202 | 0.691801 | 0.848936 | 0.762355 |
Charles Chapple Variant Catcher | Saphetor | Saphetor3 | 11 | 11 | 11 | 11 | 1 | 5 | 50 | 0.993583 | 0.971313 | 0.982322 | 0.818492 | 0.821489 | 0.819988 |
Zitong He | MySubmission2 | 11 | 11 | 11 | 10 | 1 | 5 | 49 | 0.994512 | 0.986508 | 0.990494 | 0.750626 | 0.860957 | 0.802015 | |
Shawn Williams | mySubmission_GATK | 7 | 11 | 10 | 11 | 1 | 5 | 45 | 0.363682 | 0.009959 | 0.019388 | 0.125683 | 0.014681 | 0.026291 | |
Theresa Wohlever | Whole-exome variant calling pipeline results | 7 | 6 | 5 | 5 | 0 | 5 | 28 | 0.989802 | 0.981577 | 0.985672 | 0.768957 | 0.870134 | 0.816423 | |
Patrick Brennan Variant Catcher | Nationwide Children's Hospital | NCH_SUBMISSION1 | 11 | 11 | 11 | 11 | 1 | 5 | 50 | 0.99465 | 0.98896 | 0.991797 | 0.674428 | 0.846383 | 0.750684 |
Patrick Brennan | Nationwide Children's Hospital | NCH_SUBMISSION2 | 9 | 10 | 6 | 6 | 1 | 5 | 37 | 0.99873 | 0.904229 | 0.949133 | 0.799462 | 0.757979 | 0.778168 |
Christian Iseli | Swiss Institute of Bioinformatics | SIB | 9 | 10 | 8 | 9 | 1 | 5 | 42 | 0.985602 | 0.97443 | 0.979984 | 0.753181 | 0.750585 | 0.751881 |
Richa Agarwala | NCBI | SKESA_SRPRISM | 8 | 8 | 5 | 6 | 0 | 1 | 28 | 0.32541 | 0.30702 | 0.315947 | 0.424784 | 0.416383 | 0.420542 |
Hong Chen Variant Catcher | Sentieon Inc | Sentieon_DNAseq_allmap-NA12878MOD | 11 | 11 | 11 | 11 | 1 | 5 | 50 | 0.990597 | 0.989473 | 0.990035 | 0.743829 | 0.864787 | 0.79976 |
Hong Chen Variant Catcher | Sentieon Inc | Sentieon_DNAseq_allmap_nodedup-NA12878MOD | 11 | 11 | 11 | 11 | 1 | 5 | 50 | 0.986758 | 0.989985 | 0.988369 | 0.721072 | 0.86617 | 0.786989 |
Pi Chuan Chang | DeepVariant | 8 | 10 | 9 | 9 | 1 | 5 | 42 | 0.997713 | 0.99126 | 0.994476 | 0.841122 | 0.876064 | 0.858238 | |
Pi Chuan Chang | DeepVariant_LowFrequency | 9 | 10 | 9 | 11 | 1 | 5 | 45 | 0.997256 | 0.9918 | 0.99452 | 0.813021 | 0.881277 | 0.845774 | |
Hanying Feng Variant Catcher | Sentieon Inc | Sentieon_TNscope_Tonly_allmap-NA12878MOD | 11 | 11 | 11 | 11 | 1 | 5 | 50 | 0.594368 | 0.602787 | 0.598548 | 0.261532 | 0.539566 | 0.352301 |
Hanying Feng Variant Catcher | Sentieon Inc | Sentieon_TNscope_Tonly_allmap_nodedup-NA12878MOD | 11 | 11 | 11 | 11 | 1 | 5 | 50 | 0.539536 | 0.603383 | 0.569676 | 0.227044 | 0.538502 | 0.319416 |
Hanying Feng Variant Catcher | Sentieon Inc | Sentieon_Exp-NA12878MOD | 11 | 11 | 11 | 11 | 1 | 5 | 50 | 0.920606 | 0.99004 | 0.954061 | 0.348901 | 0.857964 | 0.496069 |
Hanying Feng Variant Catcher | Sentieon Inc | Sentieon_Exp_nodedup-NA12878MOD | 11 | 11 | 11 | 11 | 1 | 5 | 50 | 0.822392 | 0.989846 | 0.898382 | 0.331927 | 0.854878 | 0.478187 |
Rongshan Yu Variant Catcher | Aginome Scientific | NA12878MOD.imp.hardfilter.recode.vcf.gz | 11 | 11 | 11 | 11 | 1 | 5 | 50 | 0.995427 | 0.985927 | 0.990654 | 0.792018 | 0.858617 | 0.823974 |
Liu Qi Variant Catcher | BIG_myPipeline-NA12878.vcf.gz | 11 | 11 | 11 | 11 | 1 | 5 | 50 | 0.599349 | 0.602261 | 0.600801 | 0.461185 | 0.608723 | 0.524782 | |
Igor Dolgalev | NYU Langone Medical Center | Bowtie2 + GATK HaplotypeCaller unfiltered | 11 | 11 | 11 | 10 | 1 | 5 | 49 | 0.995208 | 0.954788 | 0.974579 | 0.78762 | 0.826277 | 0.806485 |
Liu Qi | BIG_HXG-NA12878.vcf.gz | 11 | 11 | 10 | 10 | 0 | 5 | 47 | 0.989178 | 0.985802 | 0.987487 | 0.471407 | 0.745905 | 0.577707 | |
Igor Dolgalev | NYU Langone Medical Center | Bowtie2 + GATK HaplotypeCaller depth-filtered | 11 | 11 | 11 | 10 | 1 | 5 | 49 | 0.995289 | 0.892413 | 0.941048 | 0.785136 | 0.776702 | 0.780896 |
Sijung Yun | Yotta Biomed, LLC. | Yotta1_GRCh37_liftover_from_GRCh38_sorted | 10 | 11 | 11 | 10 | 1 | 5 | 48 | 0.992543 | 0.962503 | 0.977293 | 0.738275 | 0.830106 | 0.781502 |
Sijung Yun | Yotta Biomed, LLC. | Yotta2_GRCh37_liftover_from_GRCh38_sorted | 0 | 0 | 0 | 0 | 0 | 5 | 5 | 0.930078 | 0.960896 | 0.945236 | 0.041667 | 0.001808 | 0.003465 |
Sijung Yun | Yotta Biomed, LLC. | Yotta3_GRCh37_liftover_from_GRCh38_sorted | 10 | 11 | 11 | 10 | 1 | 5 | 48 | 0.975282 | 0.965274 | 0.970252 | 0.606772 | 0.835638 | 0.703048 |
Igor Dolgalev | NYU Langone Medical Center | BWA-MEM + GATK + SNVer | 11 | 9 | 5 | 8 | 0 | 5 | 38 | 0.983388 | 0.93052 | 0.956224 | 0.394808 | 0.467021 | 0.427889 |
Severine Catreux Variant Catcher | Edico Genome | DRAGEN_DNASeq_NA12878MOD_submission6 | 11 | 11 | 11 | 11 | 1 | 5 | 50 | 0.972624 | 0.992326 | 0.982376 | 0.705784 | 0.89917 | 0.790826 |
Severine Catreux Variant Catcher | Edico Genome | DRAGEN_DNASeq_NA12878MOD_submission7b | 11 | 11 | 11 | 11 | 1 | 5 | 50 | 0.993589 | 0.991551 | 0.992569 | 0.8195 | 0.896299 | 0.856181 |
Jean Thierrymieg | NCBI | NCBI_Magic_ThierryMieg_NA12878MOD.b.vcf.gz | 6 | 4 | 2 | 5 | 0 | 4 | 21 | 0.99067 | 0.957212 | 0.973654 | 0.733128 | 0.641277 | 0.684133 |
Joon Sang Lee Variant Catcher | Sanofi | JSLee_NA12878MOD_final_2.vcf.gz | 11 | 11 | 11 | 11 | 1 | 5 | 50 | 0.984611 | 0.959802 | 0.972048 | 0.753181 | 0.825319 | 0.787602 |
Joon Sang Lee | Sanofi | JSLee_NA12878MOD_final_3.vcf.gz | 10 | 10 | 8 | 9 | 1 | 5 | 43 | 0.99641 | 0.945757 | 0.970423 | 0.913897 | 0.728298 | 0.810609 |
Joon Sang Lee | Sanofi | JSLee_NA12878MOD_final_4.vcf.gz | 0 | 0 | 0 | 0 | 0 | 5 | 5 | 0.998844 | 0.921197 | 0.95845 | 1 | 0.000106 | 0.000213 |
The second table provides detailed variant detection information for each of the 50 injected variants from all qualified submissions. This table also specifies all injected variants with their expected VAF. In this table, VAF is displayed if the variant is present in submitted VCF for a specific entry and the VAF information was derived from the VCF file (i.e. VAF, AD/DP, or AB meta tag was available in the VCF file). For variants which were present in the VCF file, but failed to pass the filtering criteria (as defined by the filter meta tag), the variant is annotated as “filtered” with its associated VAF. Participant entries that supplied VAF data in accordance with the challenge instructions, and that detected all 50 variants reasonably close to the expected VAF values, are being recognized as Warm Up in silico VAF Spotters, indicated by the VAF Spotter icon in the table below (37 entries earned this title). These recognitions are based on the information found in raw VCF data for each entry, regardless of whether the submitter called each of the variants as above 20%. This is due to various reasons, including quality filters set for the pipeline.
Entry |
Variant 1
chr: 1 pos: 27093043 G T true vaf: 0.45 target vaf: 0.50 |
Variant 2
chr: 1 pos: 27106406 GGCT G true vaf: 0.20 target vaf: 0.20 |
Variant 3
chr: 1 pos: 51439612 AGGTGC A true vaf: 0.47 target vaf: 0.50 |
Variant 4
chr: 1 pos: 161143427 G A true vaf: 0.43 target vaf: 0.50 |
Variant 5
chr: 1 pos: 161143694 CG C true vaf: 0.24 target vaf: 0.20 |
Variant 6
chr: 1 pos: 201984364 ACGGGTGGATGGC A true vaf: 0.42 target vaf: 0.50 |
Variant 7
chr: 2 pos: 148657316 CT C true vaf: 0.22 target vaf: 0.20 |
Variant 8
chr: 2 pos: 148676143 AACCTGCCAT A true vaf: 0.44 target vaf: 0.50 |
Variant 9
chr: 2 pos: 198266831 CTTTCTG C true vaf: 0.18 target vaf: 0.20 |
Variant 10
chr: 3 pos: 41266085 CAGTCTTACCTGG C true vaf: 0.17 target vaf: 0.20 |
Variant 11
chr: 3 pos: 52442586 GATCC G true vaf: 0.42 target vaf: 0.50 |
Variant 12
chr: 3 pos: 52597407 AATATCATCAT A true vaf: 0.15 target vaf: 0.20 |
Variant 13
chr: 3 pos: 121208445 TTTA T true vaf: 0.48 target vaf: 0.50 |
Variant 14
chr: 3 pos: 186502465 CTAT C true vaf: 0.50 target vaf: 0.50 |
Variant 15
chr: 4 pos: 55152090 GAGACATCAT G true vaf: 0.18 target vaf: 0.20 |
Variant 16
chr: 4 pos: 106156565 A AT true vaf: 0.14 target vaf: 0.20 |
Variant 17
chr: 4 pos: 153244142 A AAACTCCCC true vaf: 0.13 target vaf: 0.20 |
Variant 18
chr: 5 pos: 67591073 TATCGAGAAA T true vaf: 0.17 target vaf: 0.20 |
Variant 19
chr: 5 pos: 112175182 T TCTGCTAATACC true vaf: 0.18 target vaf: 0.20 |
Variant 20
chr: 6 pos: 26158586 G GATTC true vaf: 0.21 target vaf: 0.20 |
Variant 21
chr: 7 pos: 106523590 AT A true vaf: 0.54 target vaf: 0.50 |
Variant 22
chr: 8 pos: 117874090 GCAGTGGCTGAT G true vaf: 0.44 target vaf: 0.50 |
Variant 23
chr: 9 pos: 120475316 TTTAA T true vaf: 0.21 target vaf: 0.20 |
Variant 24
chr: 9 pos: 139397775 C CGGAAAGCGG true vaf: 0.33 target vaf: 0.50 |
Variant 25
chr: 10 pos: 8111542 T TTACTGAA true vaf: 0.16 target vaf: 0.20 |
Variant 26
chr: 10 pos: 63816961 TTGCCATTGG T true vaf: 0.36 target vaf: 0.50 |
Variant 27
chr: 10 pos: 63850750 TCCAGAGTAGAC T true vaf: 0.40 target vaf: 0.50 |
Variant 28
chr: 10 pos: 89624241 CAA C true vaf: 0.41 target vaf: 0.50 |
Variant 29
chr: 10 pos: 123276898 TATTCCCC T true vaf: 0.16 target vaf: 0.20 |
Variant 30
chr: 11 pos: 32413529 G GT true vaf: 0.26 target vaf: 0.20 |
Variant 31
chr: 11 pos: 69466026 CGACGTGCGG C true vaf: 0.12 target vaf: 0.20 |
Variant 32
chr: 12 pos: 115115435 G GT true vaf: 0.17 target vaf: 0.20 |
Variant 33
chr: 13 pos: 28608148 G GTACGTGCATTTGGAAAAGTGATGAACGCAACAGCTTA true vaf: 0.53 target vaf: 0.50 |
Variant 34
chr: 13 pos: 28623570 AGTGTAGTATCCG A true vaf: 0.21 target vaf: 0.20 |
Variant 35
chr: 13 pos: 32912707 TAAAG T true vaf: 0.21 target vaf: 0.20 |
Variant 36
chr: 13 pos: 48936946 TACAGAA T true vaf: 0.43 target vaf: 0.50 |
Variant 37
chr: 16 pos: 67070639 TAGAA T true vaf: 0.12 target vaf: 0.20 |
Variant 38
chr: 16 pos: 67644795 GGAGA G true vaf: 0.50 target vaf: 0.50 |
Variant 39
chr: 16 pos: 68835746 AAAGTCACGCTG A true vaf: 0.19 target vaf: 0.20 |
Variant 40
chr: 16 pos: 68846132 C CCACCAA true vaf: 0.21 target vaf: 0.20 |
Variant 41
chr: 16 pos: 68856070 CACAGCAGA C true vaf: 0.51 target vaf: 0.50 |
Variant 42
chr: 16 pos: 68867224 C T true vaf: 0.46 target vaf: 0.50 |
Variant 43
chr: 17 pos: 29541466 TAGAGTCTTAC T true vaf: 0.15 target vaf: 0.20 |
Variant 44
chr: 17 pos: 37676280 AACAGACCCT A true vaf: 0.42 target vaf: 0.50 |
Variant 45
chr: 17 pos: 41245089 TTGGAACAACCA T true vaf: 0.47 target vaf: 0.50 |
Variant 46
chr: 17 pos: 56056604 TTGC T true vaf: 0.55 target vaf: 0.50 |
Variant 47
chr: 19 pos: 47503717 C A true vaf: 0.52 target vaf: 0.50 |
Variant 48
chr: 20 pos: 30954203 C T true vaf: 0.41 target vaf: 0.50 |
Variant 49
chr: 21 pos: 44514767 C CACTCAT true vaf: 0.46 target vaf: 0.50 |
Variant 50
chr: 22 pos: 41574281 TGCAACAGCAGCA T true vaf: 0.57 target vaf: 0.50 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
SKESA_SRPRISM | Not Found | Not Found | 1 | 1 | 0.98 | 0.98 | 1 | 1 | Not Found | Not Found | 1 | Not Found | 1 | 1 | Not Found | Not Found | Not Found | Not Found | 1 | Not Found | 0.95 | Not Found | 1 | 1 | Not Found | 1 | Not Found | 0.98 | Not Found | 1 | Not Found | Not Found | Not Found | 1 | 1 | 1 | Not Found | 1 | 1 | 1 | 1 | Not Found | Not Found | 1 | 1 | 0.98 | Not Found | Not Found | 0.98 | 1 |
B15GATK36 VAF Spotter | 0.47 | 0.23 | 0.45 | 0.47 | 0.27 | 0.37 | 0.23 | 0.41 | 0.21 | 0.18 | 0.43 | 0.14 | 0.51 | 0.5 | 0.15 | 0.15 | 0.14 | 0.18 | 0.21 | 0.21 | 0.54 | 0.39 | 0.25 | 0.37 | 0.2 | 0.34 | 0.45 | 0.42 | 0.18 | 0.28 | 0.15 | 0.19 | 0.55 | 0.21 | 0.23 | 0.44 | 0.13 | 0.46 | 0.19 | 0.24 | 0.5 | 0.52 | 0.14 | 0.41 | 0.45 | 0.44 | 0.51 | 0.43 | 0.47 | 0.58 |
B8GATK36 VAF Spotter | 0.47 | 0.23 | 0.45 | 0.47 | 0.27 | 0.37 | 0.23 | 0.41 | 0.21 | 0.18 | 0.43 | 0.14 | 0.51 | 0.5 | 0.15 | 0.15 | 0.14 | 0.18 | 0.21 | 0.21 | 0.54 | 0.39 | 0.25 | 0.37 | 0.2 | 0.34 | 0.45 | 0.42 | 0.18 | 0.28 | 0.15 | 0.19 | 0.55 | 0.21 | 0.23 | 0.44 | 0.13 | 0.46 | 0.19 | 0.24 | 0.5 | 0.52 | 0.14 | 0.41 | 0.45 | 0.44 | 0.51 | 0.43 | 0.47 | 0.58 |
Saphetor4 VAF Spotter | 0.47 | 0.23 | 0.45 | 0.47 | 0.27 | 0.37 | 0.23 | 0.39 | 0.21 | 0.18 | 0.43 | 0.13 | 0.51 | 0.5 | 0.14 | 0.15 | 0.14 | 0.17 | 0.21 | 0.22 | 0.54 | 0.36 | 0.25 | 0.37 | 0.2 | 0.34 | 0.44 | 0.41 | 0.17 | 0.28 | 0.15 | 0.19 | 0.55 | 0.21 | 0.23 | 0.45 | 0.13 | 0.46 | 0.19 | 0.24 | 0.48 | 0.52 | 0.14 | 0.39 | 0.44 | 0.44 | 0.51 | 0.43 | 0.47 | 0.52 |
BIG_CelerSNP-NA12878.vcf | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available |
BIG_HXG-NA12878.vcf.gz | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Found | Not Available | Not Available | Not Available | Not Available | Not Found | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Found | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available |
BIG_myPipeline-NA12878.vcf.gz | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available |
BIG_NGSToolkit-NA12878.vcf | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available | Not Available |
DeepVariant_LowFrequency | 0.48 | 0.25 | 0.49 | 0.44 | 0.29 (Filtered) | 0.45 | 0.23 | 0.4 | 0.2 | 0.2 | 0.44 | 0.16 | 0.53 | 0.52 | 0.2 | 0.15 | 0.13 (Filtered) | 0.18 | 0.18 | 0.21 | 0.53 | 0.4 | 0.27 | 0.35 | 0.15 (Filtered) | 0.36 | 0.49 | 0.42 | 0.21 | 0.27 | 0.21 | 0.19 (Filtered) | 0.38 | 0.25 | 0.24 | 0.48 | 0.16 (Filtered) | 0.49 | 0.23 | 0.23 | 0.54 | 0.5 | 0.17 | 0.46 | 0.5 | 0.59 | 0.51 | 0.43 | 0.47 | 0.57 |
DeepVariant | 0.48 | 0.25 (Filtered) | 0.49 | 0.44 | 0.29 (Filtered) | 0.45 | 0.23 | 0.4 | 0.2 | 0.2 | 0.44 | 0.16 (Filtered) | 0.53 | 0.52 | 0.2 | 0.15 | 0.13 (Filtered) | 0.18 | 0.18 | 0.21 | 0.53 | 0.4 | 0.27 | 0.35 | 0.15 (Filtered) | 0.36 | 0.49 | 0.42 | 0.21 | 0.27 | 0.21 | 0.19 (Filtered) | 0.38 | 0.25 | 0.24 | 0.48 | 0.16 (Filtered) | 0.49 | 0.23 | 0.23 | 0.54 | 0.5 | 0.17 (Filtered) | 0.46 | 0.5 | 0.59 | 0.51 | 0.43 | 0.47 | 0.57 |
DRAGEN_DNASeq_NA12878MOD_submission1 VAF Spotter | 0.47 | 0.23 | 0.45 | 0.47 | 0.26 | 0.37 | 0.23 | 0.4 | 0.21 | 0.18 | 0.43 | 0.14 | 0.51 | 0.5 | 0.15 | 0.15 | 0.14 | 0.18 | 0.21 | 0.21 | 0.54 | 0.39 | 0.25 | 0.37 | 0.2 | 0.34 | 0.45 | 0.42 | 0.18 | 0.28 | 0.15 | 0.19 | 0.55 | 0.21 | 0.23 | 0.45 | 0.13 | 0.46 | 0.19 | 0.24 | 0.5 | 0.52 | 0.14 | 0.41 | 0.45 | 0.44 | 0.51 | 0.43 | 0.47 | 0.54 |
DRAGEN_DNASeq_NA12878MOD_submission2 VAF Spotter | 0.47 | 0.23 | 0.45 | 0.47 | 0.26 | 0.37 | 0.23 | 0.4 | 0.21 | 0.18 | 0.43 | 0.14 | 0.51 | 0.5 | 0.15 | 0.15 | 0.14 | 0.18 | 0.21 | 0.21 | 0.54 | 0.39 | 0.25 | 0.37 | 0.2 | 0.34 | 0.45 | 0.42 | 0.18 | 0.28 | 0.15 | 0.19 | 0.55 | 0.21 | 0.23 | 0.45 | 0.13 | 0.46 | 0.19 | 0.24 | 0.5 | 0.52 | 0.14 | 0.41 | 0.45 | 0.44 | 0.51 | 0.43 | 0.47 | 0.54 |
DRAGEN_DNASeq_NA12878MOD_submission3 | 0.47 | 0.23 | 0.45 | 0.47 | 0.26 | 0.37 | 0.23 | 0.4 | 0.21 | 0.18 | 0.43 | 0.14 | 0.51 | 0.5 | 0.15 | 0.15 | 0.14 | 0.18 | 0.21 | 0.21 | 0.54 | 0.39 | 0.25 | 0.37 | 0.2 | 0.34 | 0.45 | 0.42 | 0.18 | 0.28 | 0.15 | 0.19 | 0.55 | 0.21 | 0.23 | 0.45 | 0.13 | 0.46 | 0.19 | 0.24 | 0.5 | 0.52 | 0.14 | 0.41 | 0.45 | Not Found | 0.51 | 0.43 | 0.47 | 0.54 |
DRAGEN_DNASeq_NA12878MOD_submission4 | 0.47 | 0.23 | 0.45 | 0.47 | 0.26 | 0.37 | 0.23 | 0.4 | 0.21 | 0.18 | 0.43 | 0.14 | 0.51 | 0.5 | 0.15 | 0.15 | 0.14 | 0.18 | 0.21 | 0.21 | 0.54 | 0.39 | 0.25 | 0.37 | 0.2 | 0.34 | 0.45 | 0.42 | 0.18 | 0.28 | 0.15 | 0.19 | 0.55 | 0.21 | 0.23 | 0.45 | 0.13 | 0.46 | 0.19 | 0.24 | 0.5 | 0.52 | 0.14 | 0.41 | 0.45 | Not Found | 0.51 | 0.43 | 0.47 | 0.54 |
DRAGEN_DNASeq_NA12878MOD_submission5 VAF Spotter | 0.47 | 0.23 | 0.45 | 0.47 | 0.26 | 0.37 | 0.23 | 0.4 | 0.21 | 0.18 | 0.43 | 0.14 | 0.51 | 0.5 | 0.15 | 0.15 | 0.14 | 0.18 | 0.21 | 0.21 | 0.54 | 0.39 | 0.25 | 0.37 | 0.2 | 0.34 | 0.45 | 0.42 | 0.18 | 0.28 | 0.15 | 0.19 | 0.55 | 0.21 | 0.23 | 0.45 | 0.13 | 0.46 | 0.19 | 0.24 | 0.5 | 0.52 | 0.14 | 0.41 | 0.45 | 0.44 | 0.51 | 0.43 | 0.47 | 0.54 |
DRAGEN_DNASeq_NA12878MOD_submission6 VAF Spotter | 0.47 | 0.23 | 0.45 | 0.47 | 0.26 | 0.37 | 0.23 | 0.4 | 0.21 | 0.18 | 0.43 | 0.14 | 0.51 | 0.5 | 0.15 | 0.15 | 0.14 | 0.18 | 0.21 | 0.21 | 0.54 | 0.39 | 0.25 | 0.37 | 0.2 | 0.34 | 0.45 | 0.42 | 0.18 | 0.28 | 0.15 | 0.19 | 0.55 | 0.21 | 0.23 | 0.45 | 0.13 | 0.46 | 0.19 | 0.24 | 0.5 | 0.52 | 0.14 | 0.41 | 0.45 | 0.44 | 0.51 | 0.43 | 0.47 | 0.54 |
DRAGEN_DNASeq_NA12878MOD_submission7b VAF Spotter | 0.47 | 0.23 | 0.45 | 0.47 | 0.26 | 0.37 | 0.23 | 0.4 | 0.21 | 0.18 | 0.43 | 0.14 | 0.51 | 0.5 | 0.15 | 0.15 | 0.14 | 0.18 | 0.21 | 0.21 | 0.54 | 0.39 | 0.25 | 0.37 | 0.2 | 0.34 | 0.45 | 0.42 | 0.18 | 0.28 | 0.15 | 0.19 | 0.55 | 0.21 | 0.23 | 0.45 | 0.13 | 0.46 | 0.19 | 0.24 | 0.5 | 0.52 | 0.14 | 0.41 | 0.45 | 0.44 | 0.51 | 0.43 | 0.47 | 0.54 |
Saphetor1 VAF Spotter | 0.47 | 0.23 | 0.46 | 0.47 | 0.27 | 0.37 | 0.23 | 0.4 | 0.21 | 0.18 | 0.43 | 0.14 | 0.51 | 0.5 | 0.15 | 0.15 | 0.14 | 0.18 | 0.21 | 0.21 | 0.54 | 0.39 | 0.25 | 0.37 | 0.2 | 0.34 | 0.45 | 0.42 | 0.18 | 0.28 | 0.15 | 0.19 | 0.55 | 0.21 | 0.23 | 0.45 | 0.13 | 0.46 | 0.2 | 0.24 | 0.5 | 0.52 | 0.14 | 0.41 | 0.45 | 0.44 | 0.51 | 0.43 | 0.47 | 0.54 |
Saphetor2 VAF Spotter | 0.47 | 0.23 | 0.45 | 0.47 | 0.27 | 0.37 | 0.23 | 0.4 | 0.21 | 0.18 | 0.43 | 0.14 | 0.51 | 0.5 | 0.15 | 0.15 | 0.14 | 0.18 | 0.21 | 0.21 | 0.54 | 0.39 | 0.25 | 0.37 | 0.2 | 0.34 | 0.45 | 0.42 | 0.18 | 0.28 | 0.15 | 0.19 | 0.55 | 0.21 | 0.23 | 0.45 | 0.13 | 0.46 | 0.19 | 0.24 | 0.5 | 0.52 | 0.14 | 0.41 | 0.45 | 0.44 | 0.51 | 0.43 | 0.47 | 0.54 |
Saphetor3 VAF Spotter | 0.47 | 0.23 | 0.45 | 0.47 | 0.27 | 0.37 | 0.23 | 0.4 | 0.21 | 0.18 | 0.43 | 0.14 | 0.51 | 0.5 | 0.15 | 0.15 | 0.14 | 0.18 | 0.21 | 0.21 | 0.54 | 0.39 | 0.25 | 0.37 | 0.2 | 0.34 | 0.45 | 0.42 | 0.18 | 0.28 | 0.15 | 0.19 | 0.55 | 0.21 | 0.23 | 0.45 | 0.13 | 0.46 | 0.19 | 0.24 | 0.5 | 0.52 | 0.14 | 0.41 | 0.45 | 0.44 | 0.51 | 0.43 | 0.47 | 0.54 |
MySubmission2 | 0.47 | 0.24 | 0.45 | 0.47 | 0.26 | 0.37 | 0.23 | 0.4 | 0.21 | 0.18 | 0.43 | 0.14 | 0.51 | 0.5 | 0.15 | 0.15 | 0.14 | 0.18 | 0.21 | 0.21 | 0.53 | 0.39 | 0.25 | 0.37 | 0.2 | 0.34 | 0.45 | 0.44 | 0.18 | 0.28 | 0.15 | 0.19 | 0.55 | 0.21 | 0.23 | 0.45 | 0.13 | 0.46 | 0.19 | 0.24 | 0.5 | 0.52 | Not Found | 0.41 | 0.45 | 0.44 | 0.51 | 0.43 | 0.47 | 0.54 |
Experimental Unfiltered | 0.48 | 0.22 | 0.45 | 0.46 | 0.26 | 0.37 | 0.22 | 0.4 | 0.2 | 0.18 | 0.43 | 0.13 | 0.51 | 0.51 | 0.14 | 0.15 | 0.13 | 0.17 | 0.19 | 0.21 | 0.54 | 0.36 | 0.25 | 0.37 | 0.18 | 0.33 | 0.43 | 0.42 | 0.18 | 0.28 | Not Found | 0.18 | 0.55 | 0.21 | 0.23 | 0.45 | 0.13 | 0.45 | 0.19 | 0.24 | 0.49 | 0.52 | 0.14 | 0.4 | 0.44 | 0.44 | 0.5 | 0.44 | 0.47 | 0.53 |
NCH_SUBMISSION2 | 0.47 | 0.23 | 0.45 | 0.49 | 0.27 | 0.36 | 0.21 | 0.39 | 0.21 | Not Found | 0.41 | Not Found | 0.52 | 0.5 | Not Found | Not Found | Not Found | Not Found | Not Found | 0.21 | 0.54 | 0.41 | 0.24 | 0.39 | 0.2 | 0.37 | 0.46 | 0.42 | Not Found | 0.23 | Not Found | Not Found | 0.55 | 0.22 | 0.24 | 0.44 | Not Found | 0.46 | Not Found | 0.23 | 0.5 | 0.49 | Not Found | 0.42 | 0.46 | 0.57 | 0.54 | 0.4 | 0.46 | 0.55 |
NCH_SUBMISSION1 VAF Spotter | 0.47 | 0.23 | 0.45 | 0.49 | 0.27 | 0.36 | 0.21 | 0.39 | 0.21 | 0.16 | 0.41 | 0.14 | 0.52 | 0.5 | 0.16 | 0.15 | 0.14 | 0.17 | 0.19 | 0.21 | 0.54 | 0.41 | 0.24 | 0.39 | 0.2 | 0.37 | 0.46 | 0.42 | 0.18 | 0.23 | 0.13 | 0.2 | 0.55 | 0.22 | 0.24 | 0.44 | 0.14 | 0.46 | 0.2 | 0.23 | 0.5 | 0.49 | 0.14 | 0.42 | 0.46 | 0.57 | 0.54 | 0.4 | 0.46 | 0.55 |
JLack_CCBR_Leidos_StandardPipeline_noFilter | 0.48 | 0.22 | 0.44 | 0.46 | 0.27 | 0.36 | 0.24 | 0.4 | 0.21 | 0.17 | 0.44 | 0.14 | 0.5 | 0.52 | 0.14 | 0.14 | 0.13 | 0.18 | 0.21 | 0.22 | 0.54 | 0.38 | 0.24 | 0.37 | 0.16 | 0.33 | 0.44 | 0.43 | 0.16 | 0.3 | 0.14 | 0.18 | 0.56 | 0.22 | 0.22 | 0.45 | 0.13 | 0.46 | 0.2 | 0.24 | 0.53 | 0.54 | 0.14 | 0.41 | 0.44 | 0.39 | 0.5 | 0.43 | 0.47 | 0.59 |
JLack_CCBR_Leidos_StandardPipeline_relaxed | 0.48 | 0.22 | 0.44 | 0.46 | 0.27 | 0.36 | 0.24 | 0.4 | 0.21 | 0.17 | 0.44 | 0.14 | 0.5 | 0.52 | 0.14 | 0.14 | 0.13 | 0.18 | 0.21 | 0.22 | 0.54 | 0.38 | 0.24 | 0.37 | 0.16 | 0.33 | 0.44 | 0.43 | 0.16 | 0.3 | 0.14 | 0.18 | 0.56 | 0.22 | 0.22 | 0.45 | 0.13 | 0.46 | 0.2 | 0.24 | 0.53 | 0.54 | 0.14 | 0.41 | 0.44 | 0.39 | 0.5 | 0.43 | 0.47 | 0.59 |
JSLee_NA12878MOD_final_2.vcf.gz VAF Spotter | 0.48 | 0.22 | 0.46 | 0.44 | 0.27 | 0.37 | 0.23 | 0.42 | 0.21 | 0.17 | 0.44 | 0.15 | 0.51 | 0.5 | 0.16 | 0.15 | 0.14 | 0.16 | 0.21 | 0.22 | 0.54 | 0.39 | 0.25 | 0.38 | 0.19 | 0.34 | 0.44 | 0.42 | 0.18 | 0.28 | 0.15 | 0.18 | 0.57 | 0.21 | 0.23 | 0.45 | 0.13 | 0.46 | 0.2 | 0.24 | 0.5 | 0.49 | 0.14 | 0.4 | 0.46 | 0.42 | 0.5 | 0.42 | 0.48 | 0.55 |
JSLee_NA12878MOD_final_3.vcf.gz VAF Spotter | 0.48 | 0.22 | 0.46 | 0.44 | 0.27 | 0.37 | 0.23 | 0.42 | 0.21 | 0.17 | 0.44 | Not Found | 0.51 | 0.5 | 0.16 | Not Found | Not Found | 0.16 | 0.21 | 0.22 | 0.54 | 0.39 | 0.25 | 0.38 | Not Found | 0.34 | 0.44 | 0.42 | 0.18 | 0.28 | Not Found | 0.18 | 0.57 | 0.21 | 0.23 | 0.45 | Not Found | 0.46 | 0.2 | 0.24 | 0.5 | 0.49 | Not Found | 0.4 | 0.46 | 0.42 | 0.5 | 0.42 | 0.48 | 0.55 |
JSLee_NA12878MOD_final_4.vcf.gz VAF Spotter | 0.48 | Not Found | Not Found | 0.44 | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | 0.49 | Not Found | Not Found | Not Found | Not Found | 0.5 | 0.42 | Not Found | Not Found |
KCCG_1.7.0_HC VAF Spotter | 0.48 | 0.23 | 0.45 | 0.47 | 0.27 | 0.37 | 0.23 | 0.41 | 0.21 | 0.17 | 0.43 | 0.14 | 0.51 | 0.5 | 0.15 | 0.15 | 0.14 | 0.18 | 0.21 | 0.21 | 0.54 | 0.39 | 0.25 | 0.38 | 0.2 | 0.34 | 0.45 | 0.42 | 0.18 | 0.28 | 0.15 | 0.19 | 0.56 | 0.21 | 0.23 | 0.44 | 0.13 | 0.46 | 0.19 | 0.24 | 0.5 | 0.52 | 0.14 | 0.41 | 0.45 | 0.44 | 0.51 | 0.42 | 0.47 | 0.58 |
KCCG_1.7.0_VD | 0.48 | 0.23 | 0.48 | 0.44 | 0.24 | 0.42 | 0.23 | 0.4 | 0.22 | 0.17 | 0.43 | 0.17 | 0.52 | 0.47 | 0.19 | 0.15 | Not Found | 0.18 | 0.21 | 0.21 | 0.53 | 0.41 | 0.25 | 0.38 | 0.19 | 0.36 | 0.44 | 0.42 | 0.18 | 0.27 | Not Found | 0.19 | 0.55 | 0.23 | 0.23 | 0.44 | Not Found | 0.45 | 0.21 | 0.23 | 0.5 | 0.49 | 0.15 | 0.42 | 0.49 | 0.3 | 0.51 | 0.42 | 0.47 | 0.56 |
Bowtie2 + GATK HaplotypeCaller depth-filtered | 0.47 | 0.24 | 0.45 | 0.46 | 0.27 | 0.37 | 0.23 | 0.41 | 0.21 | 0.18 | 0.43 | 0.15 | 0.51 | 0.5 | 0.15 | 0.15 | 0.14 | 0.18 | 0.2 | 0.19 | 0.54 | 0.39 | 0.25 | 0.36 | 0.2 | 0.34 | 0.45 | 0.34 | 0.18 | 0.28 | 0.15 | 0.19 | 0.42 | 0.22 | 0.23 | 0.45 | 0.13 | 0.46 | 0.2 | 0.24 | 0.5 | 0.52 | Not Found | 0.41 | 0.45 | 0.44 | 0.51 | 0.43 | 0.46 | 0.54 |
Bowtie2 + GATK HaplotypeCaller unfiltered | 0.47 | 0.24 | 0.45 | 0.46 | 0.27 | 0.37 | 0.23 | 0.41 | 0.21 | 0.18 | 0.43 | 0.15 | 0.51 | 0.5 | 0.15 | 0.15 | 0.14 | 0.18 | 0.2 | 0.19 | 0.54 | 0.39 | 0.25 | 0.36 | 0.2 | 0.34 | 0.45 | 0.34 | 0.18 | 0.28 | 0.15 | 0.19 | 0.42 | 0.22 | 0.23 | 0.45 | 0.13 | 0.46 | 0.2 | 0.24 | 0.5 | 0.52 | Not Found | 0.41 | 0.45 | 0.44 | 0.51 | 0.43 | 0.46 | 0.54 |
Challenge_submission_20170912_3 | 0.47 | 0.23 | 0.45 | 0.47 | 0.26 | 0.37 | 0.23 | 0.41 | 0.21 | 0.18 | 0.43 | 0.14 | 0.51 | 0.5 | 0.15 | 0.15 | 0.14 | 0.18 | 0.21 | 0.21 | 0.54 | 0.39 | 0.25 | 0.37 | 0.2 | 0.34 | 0.45 | 0.42 | 0.18 | 0.28 | 0.15 | 0.19 | Not Found | 0.21 | 0.23 | 0.45 | 0.13 | 0.46 | 0.19 | 0.24 | 0.5 | 0.52 | 0.14 | 0.41 | 0.45 | 0.44 | 0.51 | 0.43 | 0.47 | 0.54 |
GATK HaplotypeCaller depth-filtered VAF Spotter | 0.47 | 0.23 | 0.46 | 0.46 | 0.27 | 0.37 | 0.23 | 0.41 | 0.21 | 0.18 | 0.43 | 0.14 | 0.51 | 0.51 | 0.15 | 0.15 | 0.14 | 0.18 | 0.21 | 0.21 | 0.54 | 0.39 | 0.25 | 0.37 | 0.19 | 0.34 | 0.45 | 0.41 | 0.17 | 0.28 | 0.15 | 0.19 | 0.56 | 0.21 | 0.23 | 0.45 | 0.13 | 0.46 | 0.19 | 0.24 | 0.5 | 0.5 | 0.14 | 0.41 | 0.45 | 0.42 | 0.51 | 0.44 | 0.46 | 0.54 |
GATK HaplotypeCaller unfiltered VAF Spotter | 0.47 | 0.23 | 0.46 | 0.46 | 0.27 | 0.37 | 0.23 | 0.41 | 0.21 | 0.18 | 0.43 | 0.14 | 0.51 | 0.51 | 0.15 | 0.15 | 0.14 | 0.18 | 0.21 | 0.21 | 0.54 | 0.39 | 0.25 | 0.37 | 0.19 | 0.34 | 0.45 | 0.41 | 0.17 | 0.28 | 0.15 | 0.19 | 0.56 | 0.21 | 0.23 | 0.45 | 0.13 | 0.46 | 0.19 | 0.24 | 0.5 | 0.5 | 0.14 | 0.41 | 0.45 | 0.42 | 0.51 | 0.44 | 0.46 | 0.54 |
Test VAF Spotter | 0.47 | 0.24 | 0.45 | 0.46 | 0.25 | 0.37 | 0.23 | 0.43 | 0.2 | 0.18 | 0.42 | 0.14 | 0.51 | 0.5 | 0.15 | 0.14 | 0.15 | 0.18 | 0.21 | 0.22 | 0.55 | 0.4 | 0.25 | 0.35 | 0.19 | 0.35 | 0.42 | 0.42 | 0.18 | 0.27 | 0.14 | 0.19 | 0.56 | 0.23 | 0.23 | 0.45 | 0.12 | 0.47 | 0.19 | 0.23 | 0.5 | 0.51 | 0.15 | 0.41 | 0.45 | 0.44 | 0.52 | 0.42 | 0.48 | 0.54 |
NA12878MOD.imp.hardfilter.recode.vcf.gz VAF Spotter | 0.47 | 0.23 | 0.45 | 0.47 | 0.27 | 0.37 | 0.23 | 0.4 | 0.21 | 0.18 | 0.43 | 0.14 | 0.51 | 0.5 | 0.15 | 0.15 | 0.14 | 0.18 | 0.21 | 0.21 | 0.54 | 0.39 | 0.25 | 0.37 | 0.2 | 0.34 | 0.45 | 0.42 | 0.18 | 0.28 | 0.15 | 0.19 | 0.55 | 0.21 | 0.23 | 0.45 | 0.13 | 0.46 | 0.19 | 0.24 | 0.5 | 0.52 | 0.14 | 0.41 | 0.45 | 0.44 | 0.51 | 0.43 | 0.47 | 0.54 |
NA12878MOD.imp.v2.recode.vcf.gz VAF Spotter | 0.47 | 0.23 | 0.45 | 0.47 | 0.27 | 0.37 | 0.23 | 0.4 | 0.21 | 0.18 | 0.43 | 0.14 | 0.51 | 0.5 | 0.15 | 0.15 | 0.14 | 0.18 | 0.21 | 0.21 | 0.54 | 0.39 | 0.25 | 0.37 | 0.2 | 0.34 | 0.45 | 0.42 | 0.18 | 0.28 | 0.15 | 0.19 | 0.55 | 0.21 | 0.23 | 0.45 | 0.13 | 0.46 | 0.19 | 0.24 | 0.5 | 0.52 | 0.14 | 0.41 | 0.45 | 0.44 | 0.51 | 0.43 | 0.47 | 0.54 |
NA12878MOD.imp.v3.recode.vcf VAF Spotter | 0.47 | 0.23 | 0.45 | 0.47 | 0.27 | 0.37 | 0.23 | 0.4 | 0.21 | 0.18 | 0.43 | 0.14 | 0.51 | 0.5 | 0.15 | 0.15 | 0.14 | 0.18 | 0.21 | 0.21 | 0.54 | 0.39 | 0.25 | 0.37 | 0.2 | 0.34 | 0.45 | 0.42 | 0.18 | 0.28 | 0.15 | 0.19 | 0.55 | 0.21 | 0.23 | 0.45 | 0.13 | 0.46 | 0.19 | 0.24 | 0.5 | 0.52 | 0.14 | 0.41 | 0.45 | 0.44 | 0.51 | 0.43 | 0.47 | 0.54 |
NA12878MOD.imp.vcf.gz VAF Spotter | 0.47 | 0.23 | 0.45 | 0.47 | 0.27 | 0.37 | 0.23 | 0.4 | 0.21 | 0.18 | 0.43 | 0.14 | 0.51 | 0.5 | 0.15 | 0.15 | 0.14 | 0.18 | 0.21 | 0.21 | 0.54 | 0.39 | 0.25 | 0.37 | 0.2 | 0.34 | 0.45 | 0.42 | 0.18 | 0.28 | 0.15 | 0.19 | 0.55 | 0.21 | 0.23 | 0.45 | 0.13 | 0.46 | 0.19 | 0.24 | 0.5 | 0.52 | 0.14 | 0.41 | 0.45 | 0.44 | 0.51 | 0.43 | 0.47 | 0.54 |
Whole-exome variant calling pipeline results | 0.44 | Not Found | 0.44 | 0.44 | 0.22 | 0.36 | Not Found | 0.45 | Not Found | Not Found | 0.38 | Not Found | 0.47 | 0.47 | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | 0.54 | 0.42 | Not Found | 0.33 | Not Found | 0.35 | 0.36 | 0.4 | Not Found | 0.25 | Not Found | Not Found | Not Found | Not Found | 0.22 | 0.42 | Not Found | 0.47 | Not Found | Not Found | 0.5 | 0.46 | Not Found | 0.38 | 0.44 | 0.33 | 0.52 | 0.41 | 0.46 | 0.53 |
ADIscan_NA12878MOD_all | 0.44 | 0.18 | 0.4 | 0.46 | 0.22 | 0.42 | 0.21 | 0.45 | 0.16 | Not Found | 0.4 | 0.12 | 0.46 | 0.44 | 0.15 | 0.14 | 0.13 | 0.17 | 0.16 | 0.19 | 0.54 | 0.42 | 0.22 | 0.3 | 0.14 | 0.35 | 0.39 | 0.41 | 0.13 | 0.25 | 0.12 | 0.17 | Not Found | 0.21 | 0.21 | 0.4 | 0.1 | 0.48 | 0.19 | 0.2 | 0.47 | 0.48 | 0.12 | 0.37 | 0.45 | 0.29 | 0.51 | 0.4 | 0.44 | 0.55 |
ADIscan_NA12878MOD_conf | 0.44 | 0.18 | 0.4 | 0.46 | 0.22 | 0.42 | 0.21 | 0.45 | 0.16 | Not Found | 0.4 | 0.12 | 0.46 | 0.44 | 0.15 | 0.14 | 0.13 | 0.17 | 0.16 | 0.19 | 0.54 | 0.42 | 0.22 | 0.3 | 0.14 | 0.35 | 0.39 | 0.41 | 0.13 | 0.25 | 0.12 | 0.17 | Not Found | 0.21 | 0.21 | 0.4 | 0.1 | 0.48 | 0.19 | 0.2 | 0.47 | 0.48 | 0.12 | 0.37 | 0.45 | 0.29 | 0.51 | 0.4 | 0.44 | 0.55 |
ADIscan_NA12878MOD_filtered | 0.44 | 0.18 | 0.4 | 0.46 | 0.22 | 0.42 | 0.21 | 0.45 | 0.16 | Not Found | 0.4 | 0.12 | 0.46 | 0.44 | 0.15 | 0.14 | 0.13 | 0.17 | 0.16 | 0.19 | 0.54 | 0.42 | 0.22 | 0.3 | 0.14 | 0.35 | 0.39 | 0.41 | 0.13 | 0.25 | 0.12 | 0.17 | Not Found | 0.21 | 0.21 | 0.4 | 0.1 | 0.48 | 0.19 | 0.2 | 0.47 | 0.48 | 0.12 | 0.37 | 0.45 | 0.29 | 0.51 | 0.4 | 0.44 | 0.55 |
ADIscan_NA12878MOD_tight | 0.44 | 0.18 | 0.4 | 0.46 | 0.22 | 0.42 | 0.21 | 0.45 | 0.16 | Not Found | 0.4 | 0.12 | 0.46 | 0.44 | 0.15 | 0.14 | 0.13 | 0.17 | 0.16 | 0.19 | 0.54 | 0.42 | 0.22 | 0.3 | 0.14 | 0.35 | 0.39 | 0.41 | 0.13 | 0.25 | 0.12 | 0.17 | Not Found | 0.21 | 0.21 | 0.4 | 0.1 | 0.48 | 0.19 | 0.2 | 0.47 | 0.48 | 0.12 | 0.37 | 0.45 | 0.29 | 0.51 | 0.4 | 0.44 | 0.55 |
HULP-germ | 0.46 | 0.22 | 0.24 | 0.47 | 0.24 | 0.2 | 0.23 | 0.21 | 0.18 | 0.16 | 0.2 | 0.14 | 0.26 | 0.23 | 0.16 | 0.14 | 0.14 | 0.16 | 0.19 | 0.2 | 0.27 | 0.21 | 0.23 | 0.17 | 0.18 | 0.17 | 0.2 | 0.14 | 0.16 | 0.28 | 0.12 | 0.18 | Not Found | 0.19 | 0.22 | 0.22 | 0.11 | 0.23 | 0.17 | 0.22 | 0.25 | 0.5 | Not Found | 0.18 | 0.24 | 0.25 | 0.52 | 0.44 | 0.23 | 0.28 |
Submission1 | 0.47 | 0.24 | 0.45 | 0.47 | 0.26 | 0.37 | 0.23 | 0.4 | 0.21 | 0.18 | 0.43 | 0.14 | 0.51 | 0.5 | 0.15 | 0.15 | 0.14 | 0.18 | 0.21 | 0.21 | 0.53 | 0.39 | 0.25 | 0.37 | 0.2 | 0.34 | 0.45 | 0.44 | 0.18 | 0.28 | 0.15 | 0.19 | 0.55 | 0.21 | 0.23 | 0.45 | 0.13 | 0.46 | 0.19 | 0.24 | 0.5 | 0.52 | Not Found | 0.41 | 0.45 | 0.44 | 0.51 | 0.43 | 0.47 | 0.53 |
SeqsLab with GATK-based Parallelization | 0.47 | 0.24 | 0.45 | 0.47 | 0.26 | 0.37 | 0.23 | 0.41 | 0.21 | 0.18 | 0.43 | 0.14 | 0.51 | 0.5 | 0.15 | 0.15 | 0.14 | 0.18 | 0.21 | 0.21 | 0.54 | 0.39 | 0.25 | 0.37 | 0.2 | 0.34 | 0.45 | 0.42 | 0.18 | 0.28 | 0.15 | 0.19 | Not Found | 0.21 | 0.23 | 0.45 | 0.13 | 0.46 | 0.19 | 0.24 | 0.5 | 0.52 | 0.14 | 0.41 | 0.45 | 0.44 | 0.51 | 0.43 | 0.47 | 0.54 |
SeqsLab with GATK-based Parallelization(conf>30) | 0.47 | 0.24 | 0.45 | 0.47 | 0.26 | 0.37 | 0.23 | 0.41 | 0.21 | 0.18 | 0.43 | 0.14 | 0.51 | 0.5 | 0.15 | 0.15 | 0.14 | 0.18 | 0.21 | 0.21 | 0.54 | 0.39 | 0.25 | 0.37 | 0.2 | 0.34 | 0.45 | 0.42 | 0.18 | 0.28 | 0.15 | 0.19 | Not Found | 0.21 | 0.23 | 0.45 | 0.13 | 0.46 | 0.19 | 0.24 | 0.5 | 0.52 | 0.14 | 0.41 | 0.45 | 0.44 | 0.51 | 0.43 | 0.47 | 0.54 |
NCBI_Magic_ThierryMieg_NA12878MOD.b.vcf.gz | 0.49 | Not Found | 0.47 | 0.44 (Filtered) | 0.24 (Filtered) | 0.47 | 0.22 (Filtered) | Not Found | Not Found | 0.2 | Not Found | Not Found | 0.45 | 0.44 | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | 0.57 | Not Found | 0.22 | Not Found | Not Found | 0.38 | Not Found | 0.42 | Not Found | 0.25 | Not Found | Not Found | Not Found | 0.21 | 0.26 | 0.45 | Not Found | Not Found | 0.21 | Not Found | 0.54 | 0.5 | Not Found | Not Found | Not Found | 0.26 | 0.54 | 0.45 | Not Found | 0.59 |
BWA-MEM + GATK + SNVer | 0.47 | 0.17 | 0.29 | 0.43 | 0.2 | 0.29 | 0.19 | 0.29 | 0.16 | Not Found | 0.3 | Not Found | 0.34 | 0.32 | Not Found | 0.13 | Not Found | Not Found | 0.17 | Not Found | 0.35 | 0.27 | 0.19 | 0.22 | Not Found | 0.24 | 0.28 | 0.29 | Not Found | 0.21 | Not Found | 0.17 | Not Found | 0.18 | 0.19 | 0.3 | Not Found | 0.32 | 0.17 | 0.18 | 0.32 | 0.53 | Not Found | 0.27 | 0.3 | 0.24 | 0.48 | 0.43 | 0.32 | 0.33 |
NovoalignFreebayes_1 | 0.47 | 0.24 | 0.44 | 0.44 | 0.24 | 0.45 | 0.23 | 0.41 | 0.21 | 0.2 | 0.42 | Not Found | 0.52 | 0.49 | 0.2 | 0.14 | Not Found | 0.17 | 0.17 | 0.21 | 0.51 | 0.39 | 0.24 | 0.33 | 0.15 | 0.34 | 0.46 | 0.39 | 0.18 | 0.25 | 0.16 | 0.19 | 0.4 | 0.24 | 0.22 | 0.43 | Not Found | 0.46 | 0.24 | 0.22 | 0.52 | 0.49 | 0.15 | 0.4 | 0.47 | 0.38 | 0.5 | 0.39 | 0.47 | 0.58 |
NovoalignFreebayes_2 | 0.45 | 0.16 | 0.41 | 0.41 | 0.21 | 0.39 | 0.2 | 0.36 | 0.17 | 0.18 | 0.38 | Not Found | 0.48 | 0.45 | 0.19 | 0.13 | Not Found | 0.14 | Not Found | 0.18 | 0.48 | 0.34 | 0.21 | 0.3 | 0.14 | 0.29 | 0.45 | 0.35 | Not Found | 0.23 | Not Found | 0.13 | 0.22 | 0.16 | 0.18 | 0.38 | Not Found | 0.42 | 0.2 | 0.21 | 0.46 | 0.47 | Not Found | 0.32 | 0.42 | 0.41 | 0.49 | 0.37 | 0.43 | 0.54 |
NovoalignGATKHC_1 VAF Spotter | 0.47 | 0.24 | 0.45 | 0.47 | 0.27 | 0.36 | 0.23 | 0.4 | 0.21 | 0.17 | 0.43 | 0.14 | 0.51 | 0.5 | 0.15 | 0.15 | 0.14 | 0.18 | 0.22 | 0.21 | 0.54 | 0.39 | 0.25 | 0.39 | 0.19 | 0.34 | 0.44 | 0.42 | 0.18 | 0.28 | 0.15 | 0.19 | 0.57 | 0.21 | 0.23 | 0.46 | 0.13 | 0.46 | 0.19 | 0.24 | 0.5 | 0.52 | 0.14 | 0.4 | 0.45 | 0.42 | 0.51 | 0.42 | 0.47 | 0.54 |
NovoalignGATKHC_2 VAF Spotter | 0.47 | 0.23 | 0.45 | 0.47 | 0.27 | 0.36 | 0.23 | 0.4 | 0.21 | 0.17 | 0.42 | 0.14 | 0.51 | 0.5 | 0.15 | 0.15 | 0.14 | 0.18 | 0.22 | 0.21 | 0.54 | 0.39 | 0.25 | 0.38 | 0.19 | 0.34 | 0.45 | 0.42 | 0.18 | 0.28 | 0.15 | 0.19 | 0.56 | 0.21 | 0.23 | 0.45 | 0.13 | 0.45 | 0.19 | 0.24 | 0.5 | 0.52 | 0.14 | 0.39 | 0.45 | 0.42 | 0.51 | 0.42 | 0.47 | 0.54 |
Sentieon_DNAseq_allmap_nodedup-NA12878MOD | 0.45 | 0.21 | 0.42 | 0.46 | 0.24 | 0.36 | 0.21 | 0.45 | 0.17 | 0.16 | 0.41 | 0.11 | 0.48 | 0.49 | 0.14 | 0.14 | 0.14 | 0.17 | 0.18 | 0.2 | 0.54 | 0.42 | 0.22 | 0.33 | 0.17 | 0.34 | 0.39 | 0.42 | 0.16 | 0.26 | 0.12 | 0.17 | 0.53 | 0.2 | 0.22 | 0.43 | 0.11 | 0.48 | 0.17 | 0.21 | 0.47 | 0.48 | 0.14 | 0.39 | 0.43 | 0.41 | 0.52 | 0.41 | 0.45 | 0.54 |
Sentieon_DNAseq_allmap-NA12878MOD VAF Spotter | 0.47 | 0.23 | 0.45 | 0.47 | 0.26 | 0.37 | 0.23 | 0.41 | 0.2 | 0.18 | 0.44 | 0.12 | 0.51 | 0.5 | 0.15 | 0.15 | 0.14 | 0.18 | 0.21 | 0.21 | 0.54 | 0.39 | 0.25 | 0.36 | 0.2 | 0.34 | 0.45 | 0.42 | 0.18 | 0.28 | 0.15 | 0.19 | 0.53 | 0.21 | 0.23 | 0.45 | 0.13 | 0.46 | 0.19 | 0.24 | 0.49 | 0.53 | 0.14 | 0.4 | 0.44 | 0.44 | 0.51 | 0.43 | 0.47 | 0.54 |
Sentieon_DNAseq_nodecoy-NA12878MOD VAF Spotter | 0.47 | 0.23 | 0.45 | 0.47 | 0.26 | 0.37 | 0.23 | 0.41 | 0.21 | 0.18 | 0.43 | 0.14 | 0.51 | 0.5 | 0.15 | 0.15 | 0.14 | 0.18 | 0.21 | 0.21 | 0.54 | 0.39 | 0.25 | 0.37 | 0.2 | 0.34 | 0.45 | 0.42 | 0.18 | 0.28 | 0.15 | 0.19 | 0.55 | 0.21 | 0.23 | 0.45 | 0.13 | 0.46 | 0.19 | 0.24 | 0.5 | 0.52 | 0.14 | 0.41 | 0.45 | 0.44 | 0.51 | 0.43 | 0.47 | 0.54 |
Sentieon_DNAseq_std-NA12878MOD VAF Spotter | 0.47 | 0.23 | 0.45 | 0.47 | 0.26 | 0.37 | 0.23 | 0.41 | 0.21 | 0.18 | 0.43 | 0.14 | 0.51 | 0.5 | 0.15 | 0.15 | 0.14 | 0.18 | 0.21 | 0.21 | 0.54 | 0.39 | 0.25 | 0.37 | 0.2 | 0.34 | 0.45 | 0.42 | 0.18 | 0.28 | 0.15 | 0.19 | 0.55 | 0.21 | 0.23 | 0.45 | 0.13 | 0.46 | 0.19 | 0.24 | 0.5 | 0.52 | 0.14 | 0.41 | 0.45 | 0.44 | 0.51 | 0.43 | 0.47 | 0.54 |
Sentieon_Exp_nodedup-NA12878MOD | 0.45 | 0.21 | 0.44 | 0.46 | 0.25 | 0.36 | 0.22 | 0.46 | 0.18 | 0.17 | 0.43 | 0.13 | 0.48 | 0.49 | 0.16 | 0.14 | 0.14 | 0.17 | 0.19 | 0.21 | 0.6 | 0.42 | 0.23 | 0.36 | 0.16 | 0.36 | 0.39 | 0.44 | 0.17 | 0.26 | 0.12 | 0.17 | 0.54 | 0.21 | 0.22 | 0.44 | 0.12 | 0.48 | 0.17 | 0.22 | 0.51 | 0.48 | 0.14 | 0.41 | 0.44 | 0.41 | 0.55 | 0.44 | 0.47 | 0.55 |
Sentieon_Exp-NA12878MOD VAF Spotter | 0.48 | 0.24 | 0.45 | 0.48 | 0.27 | 0.37 | 0.23 | 0.42 | 0.22 | 0.18 | 0.47 | 0.14 | 0.51 | 0.52 | 0.16 | 0.15 | 0.15 | 0.18 | 0.21 | 0.21 | 0.57 | 0.39 | 0.26 | 0.39 | 0.18 | 0.35 | 0.45 | 0.45 | 0.2 | 0.28 | 0.15 | 0.19 | 0.52 | 0.22 | 0.23 | 0.47 | 0.13 | 0.46 | 0.2 | 0.24 | 0.52 | 0.53 | 0.14 | 0.42 | 0.45 | 0.44 | 0.55 | 0.46 | 0.49 | 0.55 |
Sentieon_TNscope_Tonly_allmap_nodedup-NA12878MOD | 0.45 | 0.21 | 0.44 | 0.46 | 0.25 | 0.36 | 0.22 | 0.46 | 0.18 | 0.17 | 0.43 | 0.13 | 0.48 | 0.49 | 0.16 | 0.14 | 0.14 | 0.17 | 0.19 | 0.21 | 0.6 | 0.42 | 0.23 | 0.36 | 0.16 | 0.36 | 0.39 | 0.44 | 0.17 | 0.26 | 0.12 | 0.17 | 0.54 | 0.21 | 0.22 | 0.44 | 0.12 | 0.48 | 0.17 | 0.22 | 0.51 | 0.48 | 0.14 | 0.41 | 0.44 | 0.41 | 0.55 | 0.44 | 0.47 | 0.55 |
Sentieon_TNscope_Tonly_allmap-NA12878MOD VAF Spotter | 0.48 | 0.24 | 0.45 | 0.48 | 0.27 | 0.37 | 0.23 | 0.42 | 0.22 | 0.18 | 0.47 | 0.14 | 0.51 | 0.52 | 0.16 | 0.15 | 0.15 | 0.18 | 0.21 | 0.21 | 0.57 | 0.39 | 0.26 | 0.39 | 0.18 | 0.35 | 0.45 | 0.45 | 0.2 | 0.28 | 0.15 | 0.19 | 0.52 | 0.22 | 0.23 | 0.47 | 0.13 | 0.46 | 0.2 | 0.24 | 0.52 | 0.53 | 0.14 | 0.42 | 0.45 | 0.44 | 0.55 | 0.46 | 0.49 | 0.55 |
Sentieon_TNscope_Tonly_nodecoy-NA12878MOD VAF Spotter | 0.48 | 0.24 | 0.45 | 0.48 | 0.28 | 0.37 | 0.23 | 0.42 | 0.22 | 0.18 | 0.46 | 0.15 | 0.52 | 0.52 | 0.16 | 0.15 | 0.15 | 0.18 | 0.21 | 0.21 | 0.57 | 0.4 | 0.26 | 0.38 | 0.18 | 0.35 | 0.44 | 0.45 | 0.2 | 0.28 | 0.15 | 0.19 | 0.54 | 0.22 | 0.23 | 0.47 | 0.13 | 0.47 | 0.2 | 0.24 | 0.53 | 0.53 | 0.15 | 0.42 | 0.46 | 0.44 | 0.55 | 0.46 | 0.49 | 0.55 |
Sentieon_TNscope_Tonly_std-NA12878MOD VAF Spotter | 0.48 | 0.24 | 0.45 | 0.48 | 0.28 | 0.37 | 0.23 | 0.42 | 0.22 | 0.18 | 0.46 | 0.15 | 0.52 | 0.52 | 0.16 | 0.15 | 0.15 | 0.18 | 0.21 | 0.21 | 0.57 | 0.4 | 0.26 | 0.38 | 0.18 | 0.35 | 0.44 | 0.45 | 0.2 | 0.28 | 0.15 | 0.19 | 0.54 | 0.22 | 0.23 | 0.47 | 0.13 | 0.47 | 0.2 | 0.24 | 0.53 | 0.53 | 0.15 | 0.42 | 0.46 | 0.44 | 0.55 | 0.46 | 0.49 | 0.55 |
SGI_1st_result VAF Spotter | 0.47 (Filtered) | 0.23 | 0.46 (Filtered) | 0.47 | 0.26 (Filtered) | 0.37 | 0.23 (Filtered) | 0.41 | 0.21 (Filtered) | 0.18 (Filtered) | 0.43 | 0.14 (Filtered) | 0.51 (Filtered) | 0.5 | 0.15 (Filtered) | 0.15 (Filtered) | 0.14 (Filtered) | 0.18 | 0.21 (Filtered) | 0.21 | 0.54 | 0.39 | 0.25 (Filtered) | 0.37 | 0.2 (Filtered) | 0.34 (Filtered) | 0.44 | 0.42 | 0.18 (Filtered) | 0.28 (Filtered) | 0.15 | 0.19 (Filtered) | 0.58 (Filtered) | 0.21 (Filtered) | 0.23 (Filtered) | 0.45 | 0.13 (Filtered) | 0.46 | 0.19 (Filtered) | 0.24 | 0.5 | 0.52 | 0.14 (Filtered) | 0.41 | 0.45 (Filtered) | 0.44 (Filtered) | 0.51 | 0.43 | 0.47 | 0.54 |
SGI_2nd_filtration VAF Spotter | 0.47 | 0.23 | 0.46 | 0.47 | 0.26 (Filtered) | 0.37 | 0.23 (Filtered) | 0.41 | 0.21 | 0.18 (Filtered) | 0.43 | 0.14 (Filtered) | 0.51 (Filtered) | 0.5 | 0.15 (Filtered) | 0.15 (Filtered) | 0.14 (Filtered) | 0.18 | 0.21 | 0.21 | 0.54 | 0.39 | 0.25 | 0.37 | 0.2 (Filtered) | 0.34 | 0.44 | 0.42 | 0.17 (Filtered) | 0.28 | 0.15 | 0.2 (Filtered) | 0.58 (Filtered) | 0.21 | 0.23 (Filtered) | 0.45 | 0.13 (Filtered) | 0.46 | 0.19 (Filtered) | 0.24 | 0.5 | 0.52 | 0.14 (Filtered) | 0.41 | 0.45 | 0.44 (Filtered) | 0.51 | 0.43 | 0.47 | 0.54 |
SGI_4th_filtration VAF Spotter | 0.47 | 0.23 (Filtered) | 0.46 | 0.47 | 0.26 | 0.37 | 0.23 | 0.41 | 0.2 | 0.18 | 0.43 | 0.14 | 0.51 (Filtered) | 0.52 (Filtered) | 0.15 (Filtered) | 0.15 | 0.14 | 0.18 | 0.21 | 0.21 | 0.53 | 0.38 | 0.24 | 0.38 (Filtered) | 0.18 | 0.34 | 0.43 | 0.42 | 0.17 | 0.26 | 0.15 (Filtered) | 0.17 | 0.58 | 0.2 (Filtered) | 0.23 | 0.45 | 0.11 | 0.46 | 0.2 | 0.24 | 0.49 | 0.53 | 0.14 | 0.41 | 0.45 | 0.43 (Filtered) | 0.49 | 0.43 | 0.47 | 0.59 |
SGI_3rd_filtration_rere | 0.47 | 0.23 (Filtered) | Not Available | 0.47 | Not Available | Not Available | Not Available | Not Available | 0.21 | 0.18 (Filtered) | Not Available | 0.14 (Filtered) | Not Available | Not Available | 0.15 (Filtered) | 0.15 (Filtered) | 0.14 (Filtered) | 0.18 | 0.21 | 0.21 | Not Available | Not Available | Not Available | Not Available | 0.2 (Filtered) | Not Available | 0.44 | Not Available | 0.17 (Filtered) | Not Available | 0.15 (Filtered) | 0.2 (Filtered) | 0.58 (Filtered) | Not Available | Not Available | Not Available | 0.13 (Filtered) | Not Available | Not Available | Not Available | Not Available | 0.52 | 0.14 (Filtered) | Not Available | Not Available | 0.44 (Filtered) | 0.51 | 0.43 | Not Available | 0.54 |
SIB | 0.45 | 0.2 | 0.42 | 0.44 | 0.22 | 0.41 | 0.23 | 0.39 | 0.19 | 0.18 | 0.42 | Not Found | 0.47 | 0.45 | 0.18 | Not Found | Not Found | 0.82 | Not Found | 0.2 | 0.48 | 0.4 | 0.2 | 0.29 | Not Found | 0.34 | 0.4 | 0.36 | 0.17 | 0.26 | Not Found | Not Found | 0.69 | 0.22 | 0.24 | 0.39 | Not Found | 0.45 | 0.2 | 0.21 | 0.48 | 0.49 | 0.2 | 0.33 | 0.45 | 0.23 | 0.53 | 0.44 | 0.44 | 0.51 |
MySubmission1 | 0.47 | 0.24 | 0.45 | 0.47 | 0.26 | 0.37 | 0.23 | 0.4 | 0.21 | 0.18 | 0.43 | 0.14 | 0.51 | 0.5 | 0.15 | 0.15 | 0.14 | 0.18 | 0.21 | 0.21 | 0.53 | 0.39 | 0.25 | 0.37 | 0.2 | 0.34 | 0.45 | 0.44 | 0.18 | 0.28 | 0.15 | 0.19 | 0.55 | 0.21 | 0.23 | 0.45 | 0.13 | 0.46 | 0.19 | 0.24 | 0.5 | 0.52 | Not Available | 0.41 | 0.45 | 0.44 | 0.51 | 0.43 | 0.47 | 0.53 |
mySubmission_GATK | 0.47 | 0.23 (Filtered) | 0.45 | 0.47 | 0.26 | 0.37 | 0.23 | 0.41 | 0.2 | 0.18 | 0.44 | 0.14 | 0.51 (Filtered) | 0.52 (Filtered) | 0.15 | 0.15 | 0.14 | 0.18 | 0.21 | 0.21 | 0.53 | 0.38 | 0.24 | 0.38 | 0.18 | 0.34 | 0.45 | 0.43 | 0.18 | 0.26 | 0.15 (Filtered) | 0.16 | 0.58 | 0.2 | 0.23 | 0.45 | 0.12 | 0.47 | 0.2 | 0.24 | 0.49 | 0.51 | 0.07 | 0.41 | 0.45 | Not Found | 0.49 | 0.43 | 0.47 | 0.28 |
Yotta1_GRCh37_liftover_from_GRCh38_sorted VAF Spotter | 0.47 | 0.23 | 0.45 | 0.47 | 0.27 | 0.37 | 0.23 | 0.41 | 0.21 | 0.18 | 0.43 | 0.14 | 0.51 | 0.5 | 0.15 | 0.15 | 0.14 | 0.18 | 0.21 | 0.21 | 0.54 | 0.39 | 0.25 | 0.37 | 0.2 | 0.34 | 0.45 | 0.42 (Filtered) | 0.18 | 0.28 | 0.15 | 0.19 | 0.55 | 0.21 | 0.23 | 0.44 | 0.13 | 0.46 | 0.19 | 0.24 | 0.5 | 0.52 | 0.14 (Filtered) | 0.41 | 0.45 | 0.44 | 0.51 | 0.43 | 0.57 | 0.58 |
Yotta2_GRCh37_liftover_from_GRCh38_sorted | 0.45 | Not Found | Not Found | 0.44 | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | Not Found | 0.46 | Not Found | Not Found | Not Found | Not Found | 0.52 | 0.42 | Not Found | Not Found |
Yotta3_GRCh37_liftover_from_GRCh38_sorted VAF Spotter | 0.47 | 0.23 | 0.45 | 0.47 | 0.27 | 0.37 | 0.23 | 0.41 | 0.21 | 0.18 | 0.43 | 0.14 | 0.51 | 0.5 | 0.15 | 0.15 | 0.14 | 0.18 | 0.21 | 0.21 | 0.54 | 0.39 | 0.25 | 0.37 | 0.2 | 0.34 | 0.45 | 0.42 (Filtered) | 0.18 | 0.28 | 0.15 | 0.19 | 0.55 | 0.21 | 0.23 | 0.44 | 0.13 | 0.46 | 0.19 | 0.24 | 0.5 | 0.52 | 0.14 (Filtered) | 0.41 | 0.45 | 0.44 | 0.51 | 0.43 | 0.57 | 0.58 |
G3GATK36 | 0.47 | 0.23 | 0.45 | 0.46 | 0.27 | 0.36 | 0.23 | 0.4 | 0.2 | 0.18 | 0.43 | 0.14 | 0.51 | 0.5 | 0.15 | 0.15 | 0.14 | 0.18 | 0.22 | 0.21 | 0.53 | 0.39 | 0.25 | 0.37 | 0.2 | 0.34 | 0.44 | 0.42 | 0.18 | 0.28 | 0.15 | 0.2 | 0.29 | 0.21 | 0.23 | 0.44 | 0.13 | 0.46 | 0.19 | 0.24 | 0.5 | 0.51 | 0.13 | 0.41 | 0.45 | 0.44 | 0.51 | 0.44 | 0.47 | 0.58 |
HULP-mosaic | 0.44 | 0.18 | 0.38 | 0.44 (Filtered) | Not Found | 0.35 | 0.22 | 0.39 | 0.16 | 0.18 (Filtered) | 0.35 | Not Found | 0.5 | 0.43 | 0.17 | 0.14 | Not Found | 0.13 (Filtered) | Not Found | 0.17 (Filtered) | 0.55 | 0.37 | 0.19 | 0.26 | 0.12 | 0.29 | 0.31 | 0.38 | 0.14 | 0.24 | 0.1 (Filtered) | 0.16 | Not Found | 0.18 | 0.21 | 0.36 | 0.11 (Filtered) | 0.44 | 0.15 | 0.2 | 0.42 (Filtered) | 0.48 | Not Found | 0.3 (Filtered) | 0.38 | 0.35 | 0.49 | 0.4 (Filtered) | 0.45 | 0.47 |