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broadinstitute / gatk

Official code repository for GATK versions 4 and up
https://software.broadinstitute.org/gatk
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A representative ticket to track my work documenting tools from the protected repo, #3055

Closed sooheelee closed 7 years ago

sooheelee commented 7 years ago

since I haven't tracked my PRs with story points.

1   AllelicCNV      18-May  https://github.com/broadinstitute/gatk-protected/blob/465d9fe90cd26d55cca440e14cbcf5dd9fd50566/src/main/java/org/broadinstitute/hellbender/tools/exome/AllelicCNV.java  scripts/cnv_wdl/somatic/cnv_somatic_allele_fraction_pair_workflow.wdl   https://github.com/broadinstitute/gatk-protected/pull/1049  yes 
4   CalculateTargetCoverage     19-May  https://github.com/broadinstitute/gatk-protected/blob/e1ffbff498db40c894105c06a41b443859b58a04/src/main/java/org/broadinstitute/hellbender/tools/exome/CalculateTargetCoverage.java scripts/cnv_wdl/somatic/cnv_somatic_tasks.wdl   https://github.com/broadinstitute/gatk-protected/pull/1067  yes 
28  SparkGenomeReadCounts       19-May  https://github.com/broadinstitute/gatk-protected/blob/465d9fe90cd26d55cca440e14cbcf5dd9fd50566/src/main/java/org/broadinstitute/hellbender/tools/genome/SparkGenomeReadCounts.java  scripts/cnv_wdl/somatic/cnv_somatic_tasks.wdl   https://github.com/broadinstitute/gatk-protected/pull/1068  yes 
7   CombineReadCounts       19-May  https://github.com/broadinstitute/gatk-protected/blob/3e6142ad4eb23d4d9227fafd8e52b498263b4369/src/main/java/org/broadinstitute/hellbender/tools/exome/CombineReadCounts.java   scripts/cnv_wdl/somatic/cnv_somatic_panel_workflow.wdl  https://github.com/broadinstitute/gatk-protected/pull/1072  yes 
13  CreatePanelOfNormals        19-May  https://github.com/broadinstitute/gatk-protected/blob/e1ffbff498db40c894105c06a41b443859b58a04/src/main/java/org/broadinstitute/hellbender/tools/exome/CreatePanelOfNormals.java    scripts/cnv_wdl/somatic/cnv_somatic_panel_workflow.wdl  https://github.com/broadinstitute/gatk-protected/pull/1073  yes 
20  NormalizeSomaticReadCounts      19-May  https://github.com/broadinstitute/gatk-protected/blob/e1ffbff498db40c894105c06a41b443859b58a04/src/main/java/org/broadinstitute/hellbender/tools/exome/NormalizeSomaticReadCounts.java  scripts/cnv_wdl/somatic/cnv_somatic_copy_ratio_bam_workflow.wdl https://github.com/broadinstitute/gatk-protected/pull/1074  yes 
25  PerformSegmentation     19-May  https://github.com/broadinstitute/gatk-protected/blob/465d9fe90cd26d55cca440e14cbcf5dd9fd50566/src/main/java/org/broadinstitute/hellbender/tools/exome/PerformSegmentation.java scripts/cnv_wdl/somatic/cnv_somatic_copy_ratio_bam_workflow.wdl https://github.com/broadinstitute/gatk-protected/pull/1075  yes 
27  PlotSegmentedCopyRatio      21-May  https://github.com/broadinstitute/gatk-protected/blob/e1ffbff498db40c894105c06a41b443859b58a04/src/main/java/org/broadinstitute/hellbender/tools/exome/plotting/PlotSegmentedCopyRatio.java scripts/cnv_wdl/somatic/cnv_somatic_copy_ratio_bam_workflow.wdl https://github.com/broadinstitute/gatk-protected/pull/1077  yes 
5   CallSegments        21-May  https://github.com/broadinstitute/gatk-protected/blob/465d9fe90cd26d55cca440e14cbcf5dd9fd50566/src/main/java/org/broadinstitute/hellbender/tools/exome/CallSegments.java    scripts/cnv_wdl/somatic/cnv_somatic_copy_ratio_bam_workflow.wdl https://github.com/broadinstitute/gatk-protected/pull/1078  yes 
2   AnnotateTargets     21-May  https://github.com/broadinstitute/gatk-protected/blob/465d9fe90cd26d55cca440e14cbcf5dd9fd50566/src/main/java/org/broadinstitute/hellbender/tools/exome/AnnotateTargets.java scripts/cnv_wdl/somatic/cnv_somatic_tasks.wdl   https://github.com/broadinstitute/gatk-protected/pull/1079  yes 
8   ConvertACNVResults  yes 5/22 Lee    21-May  https://github.com/broadinstitute/gatk-protected/blob/465d9fe90cd26d55cca440e14cbcf5dd9fd50566/src/main/java/org/broadinstitute/hellbender/tools/exome/ConvertACNVResults.java  scripts/cnv_wdl/somatic/cnv_somatic_allele_fraction_pair_workflow.wdl   https://github.com/broadinstitute/gatk-protected/pull/1080  yes 
9   ConvertBedToTargetFile      done    https://github.com/broadinstitute/gatk-protected/blob/465d9fe90cd26d55cca440e14cbcf5dd9fd50566/src/main/java/org/broadinstitute/hellbender/tools/exome/convertbed/ConvertBedToTargetFile.java   no but mentioned in scripts/cnv_wdl/somatic/README.md   https://github.com/broadinstitute/gatk-protected/pull/1082  yes 
21  PadTargets      done    https://github.com/broadinstitute/gatk-protected/blob/465d9fe90cd26d55cca440e14cbcf5dd9fd50566/src/main/java/org/broadinstitute/hellbender/tools/exome/PadTargets.java  scripts/cnv_wdl/somatic/cnv_somatic_tasks.wdl   https://github.com/broadinstitute/gatk-protected/pull/1093  yes 
11  CorrectGCBias       5/30    https://github.com/broadinstitute/gatk-protected/blob/465d9fe90cd26d55cca440e14cbcf5dd9fd50566/src/main/java/org/broadinstitute/hellbender/tools/exome/gcbias/CorrectGCBias.java    scripts/cnv_wdl/somatic/cnv_somatic_tasks.wdl   https://github.com/broadinstitute/gatk-protected/pull/1118  yes 
22  PerformAlleleFractionSegmentation   yes 5/30/2017, 6/3/2017 https://github.com/broadinstitute/gatk-protected/blob/087505afd217d32589cda152ac9ee4e7a7061572/src/main/java/org/broadinstitute/hellbender/tools/exome/segmentation/PerformAlleleFractionSegmentation.java  no  https://github.com/broadinstitute/gatk-protected/pull/1120  yes, but    https://github.com/broadinstitute/gatk/pull/2811
23  PerformCopyRatioSegmentation    yes 5/30    https://github.com/broadinstitute/gatk-protected/blob/087505afd217d32589cda152ac9ee4e7a7061572/src/main/java/org/broadinstitute/hellbender/tools/exome/segmentation/PerformCopyRatioSegmentation.java   no  https://github.com/broadinstitute/gatk-protected/pull/1121  yes no example command
24  PerformJointSegmentation    yes 5/30    https://github.com/broadinstitute/gatk-protected/blob/087505afd217d32589cda152ac9ee4e7a7061572/src/main/java/org/broadinstitute/hellbender/tools/exome/segmentation/PerformJointSegmentation.java   no  https://github.com/broadinstitute/gatk-protected/pull/1122  yes 
26  PlotACNVResults     5/30    https://github.com/broadinstitute/gatk-protected/blob/e1ffbff498db40c894105c06a41b443859b58a04/src/main/java/org/broadinstitute/hellbender/tools/exome/plotting/PlotACNVResults.java    scripts/cnv_wdl/somatic/cnv_somatic_allele_fraction_pair_workflow.wdl   https://github.com/broadinstitute/gatk-protected/pull/1123  yes needs review in 2nd round
18  GetBayesianHetCoverage      5/30    https://github.com/broadinstitute/gatk-protected/blob/91336c9aefb077d1dc7daf7aaae3a8dc3e007ffe/src/main/java/org/broadinstitute/hellbender/tools/exome/GetBayesianHetCoverage.java  scripts/cnv_wdl/somatic/cnv_somatic_allele_fraction_pair_workflow.wdl   https://github.com/broadinstitute/gatk-protected/pull/1125  yes https://github.com/broadinstitute/gatk/pull/2812
19  GetHetCoverage      5/30    https://github.com/broadinstitute/gatk-protected/blob/91336c9aefb077d1dc7daf7aaae3a8dc3e007ffe/src/main/java/org/broadinstitute/hellbender/tools/exome/GetHetCoverage.java  no  https://github.com/broadinstitute/gatk-protected/pull/1127  yes continue discussion about modes with Sam; add in example tumor hets file (in my scratch space)
29  TargetCoverageSexGenotyper  yes done    https://github.com/broadinstitute/gatk-protected/blob/e1ffbff498db40c894105c06a41b443859b58a04/src/main/java/org/broadinstitute/hellbender/tools/exome/sexgenotyper/TargetCoverageSexGenotyper.java no; see forwarded email https://github.com/broadinstitute/gatk-protected/pull/1102  yes 
17  GermlineCNVCaller   yes done    https://github.com/broadinstitute/gatk-protected/blob/e481e8966cf0cac48bb032b84d31835d4ccced0a/src/main/java/org/broadinstitute/hellbender/tools/coveragemodel/germline/GermlineCNVCaller.java  no  https://github.com/broadinstitute/gatk-protected/pull/1096  yes 
12  CreateAllelicPanelOfNormals yes 5/30    https://github.com/broadinstitute/gatk-protected/blob/e1ffbff498db40c894105c06a41b443859b58a04/src/main/java/org/broadinstitute/hellbender/tools/exome/CreateAllelicPanelOfNormals.java no  https://github.com/broadinstitute/gatk-protected/pull/1128  yes no example command
6   CollectAllelicCounts        5/30    https://github.com/broadinstitute/gatk-protected/blob/e1ffbff498db40c894105c06a41b443859b58a04/src/main/java/org/broadinstitute/hellbender/tools/copynumber/CollectAllelicCounts.java   no  https://github.com/broadinstitute/gatk-protected/pull/1128  yes 
16  EvaluateCopyNumberTriStateCalls internal    5/30    https://github.com/broadinstitute/gatk-protected/blob/86e725d850d129822ef4b5024f8cc46ac9ff580a/src/main/java/org/broadinstitute/hellbender/tools/exome/eval/EvaluateCopyNumberTriStateCalls.java    no  https://github.com/broadinstitute/gatk-protected/pull/1129  yes 
10  ConvertGSVariantsToSegments internal    5/30    https://github.com/broadinstitute/gatk-protected/blob/86e725d850d129822ef4b5024f8cc46ac9ff580a/src/main/java/org/broadinstitute/hellbender/tools/exome/eval/ConvertGSVariantsToSegments.java    no  https://github.com/broadinstitute/gatk-protected/pull/1117  yes needs review in 2nd round
30  XHMMSegmentCaller   internal    5/30    https://github.com/broadinstitute/gatk-protected/blob/3e6142ad4eb23d4d9227fafd8e52b498263b4369/src/main/java/org/broadinstitute/hellbender/tools/exome/germlinehmm/xhmm/XHMMSegmentCaller.java  no  https://github.com/broadinstitute/gatk-protected/pull/1129  yes 
31  XHMMSegmentGenotyper    internal    5/30    https://github.com/broadinstitute/gatk-protected/blob/86e725d850d129822ef4b5024f8cc46ac9ff580a/src/main/java/org/broadinstitute/hellbender/tools/exome/germlinehmm/xhmm/XHMMSegmentGenotyper.java   no  https://github.com/broadinstitute/gatk-protected/pull/1129  yes 
15  DetectCoverageDropout   ARCHIVE 5/30    https://github.com/broadinstitute/gatk-protected/blob/465d9fe90cd26d55cca440e14cbcf5dd9fd50566/src/main/java/org/broadinstitute/hellbender/tools/exome/detectcoveragedropout/DetectCoverageDropout.java no  https://github.com/broadinstitute/gatk-protected/pull/1130      1
14  DecomposeSingularValues ARCHIVE 5/30    https://github.com/broadinstitute/gatk-protected/blob/465d9fe90cd26d55cca440e14cbcf5dd9fd50566/src/main/java/org/broadinstitute/hellbender/tools/exome/DecomposeSingularValues.java no  https://github.com/broadinstitute/gatk-protected/pull/1130      
3   CalculatePulldownPhasePosteriors    ARCHIVE 5/30    https://github.com/broadinstitute/gatk-protected/blob/465d9fe90cd26d55cca440e14cbcf5dd9fd50566/src/main/java/org/broadinstitute/hellbender/tools/exome/CalculatePulldownPhasePosteriors.java    no  https://github.com/broadinstitute/gatk-protected/pull/1130  
46  Mutect2     6/4/2017    https://github.com/broadinstitute/gatk-protected/blob/91336c9aefb077d1dc7daf7aaae3a8dc3e007ffe/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2.java    scripts/mutect2_wdl/mutect2_multi_sample.wdl and more   https://github.com/broadinstitute/gatk/pull/2816    yes 
35  CalculateContamination      6/5/2017    https://github.com/broadinstitute/gatk-protected/blob/2bf35790393332da5414b42ec6dca813fcc63202/src/main/java/org/broadinstitute/hellbender/tools/walkers/contamination/CalculateContamination.java  scripts/mutect2_wdl/mutect2.wdl https://github.com/broadinstitute/gatk/pull/3026        3
40  CreateSomaticPanelOfNormals     6/5/2017    https://github.com/broadinstitute/gatk-protected/blob/7cbebedf49e8fcff1cb95d49608d6cb5275f4900/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/CreateSomaticPanelOfNormals.java    no  https://github.com/broadinstitute/gatk/pull/2999    yes 
41  FilterByOrientationBias BUG-->experimental and beta (SHL)   6/5/2017    https://github.com/broadinstitute/gatk-protected/blob/5c246c6a1dc92a608cd5dd8b98656ce735980161/src/main/java/org/broadinstitute/hellbender/tools/exome/FilterByOrientationBias.java scripts/mutect2_wdl/mutect2.wdl https://github.com/broadinstitute/gatk/pull/3031        4
42  FilterMutectCalls       6/5/2017    https://github.com/broadinstitute/gatk-protected/blob/1598141227de51157695a48856950b52c7a1f6b8/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/FilterMutectCalls.java  scripts/mutect2_wdl/mutect2.wdl https://github.com/broadinstitute/gatk/pull/3028    yes 
48  SplitIntervals      6/5/2017    https://github.com/broadinstitute/gatk-protected/blob/ec40da398e4185fa8fb0c62453304e8315f8f4e1/src/main/java/org/broadinstitute/hellbender/tools/walkers/SplitIntervals.java    scripts/mutect2_wdl/mutect2.wdl https://github.com/broadinstitute/gatk/pull/3032    yes Default value: INTERVAL_SUBDIVISION. warn users to be careful when dividing lengthy genomic intervals. Perhaps it would be wise to specify the workflow in which this tool would be used. Something for the second pass.
44  GetPileupSummaries  beta; helper tool for CalculateContamination    6/5/2017    https://github.com/broadinstitute/gatk-protected/blob/2bf35790393332da5414b42ec6dca813fcc63202/src/main/java/org/broadinstitute/hellbender/tools/walkers/contamination/GetPileupSummaries.java  scripts/mutect2_wdl/mutect2.wdl https://github.com/broadinstitute/gatk/pull/3006    yes 
33  AnnotateVcfWithBamDepth internal (DB)   5/30    https://github.com/broadinstitute/gatk-protected/blob/e6278def94038d76339d0fd95ce2badb3bc44a22/src/main/java/org/broadinstitute/hellbender/tools/walkers/validation/AnnotateVcfWithBamDepth.java    scripts/mutect2_wdl/unsupported/hapmap_sensitivity_truth.wdl    https://github.com/broadinstitute/gatk-protected/pull/1131  yes 
34  AnnotateVcfWithExpectedAlleleFraction   internal (DB)   5/30    https://github.com/broadinstitute/gatk-protected/blob/e6278def94038d76339d0fd95ce2badb3bc44a22/src/main/java/org/broadinstitute/hellbender/tools/walkers/validation/AnnotateVcfWithExpectedAlleleFraction.java  scripts/mutect2_wdl/unsupported/hapmap_sensitivity_truth.wdl    https://github.com/broadinstitute/gatk-protected/pull/1131  yes 
37  CalculateMixingFractions    internal (DB)   5/30    https://github.com/broadinstitute/gatk-protected/blob/e6278def94038d76339d0fd95ce2badb3bc44a22/src/main/java/org/broadinstitute/hellbender/tools/walkers/validation/CalculateMixingFractions.java   scripts/mutect2_wdl/unsupported/hapmap_sensitivity_truth.wdl    https://github.com/broadinstitute/gatk-protected/pull/1131  yes 
47  RemoveNearbyIndels  internal (DB)   5/30    https://github.com/broadinstitute/gatk-protected/blob/e6278def94038d76339d0fd95ce2badb3bc44a22/src/main/java/org/broadinstitute/hellbender/tools/walkers/validation/RemoveNearbyIndels.java scripts/mutect2_wdl/unsupported/hapmap_sensitivity_truth.wdl    https://github.com/broadinstitute/gatk-protected/pull/1131  yes

This is also at https://docs.google.com/a/broadinstitute.org/spreadsheets/d/15xviLwYUjU82MtYwxxPINiJAkovmaHpRGhqkghiEATQ/edit?usp=sharing.

sooheelee commented 7 years ago

For this first-pass documentation, the goal was to add a @DocumentedFeature tag only. I also added in example use commands from the repo's WDL scripts, if available, or scoured the integration test for an example command. Testing of the commands was extremely limited. Some tools required discussion to decide how to archive. Finally, I completely overhauled the Mutect2 documentation, which reflected GATK3's M2.