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Migrate CleanVcf into GATK#733

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kjaisingh wants to merge 46 commits intomainbroadinstitute/gatk-sv:mainfrom kj_sv_cleanvcfbroadinstitute/gatk-sv:kj_sv_cleanvcfCopy head branch name to clipboard

+756-2,355

Commits

Commits on Oct 17, 2024

• Initial commit

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  be51214

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Commits on Oct 30, 2024

• Merge branch 'main' into kj_sv_cleanvcf

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  28d2062

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Commits on Oct 31, 2024

• E2E working in local integration tests

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  d20d5b8

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Commits on Nov 1, 2024

• Furhter changes - reverted changes to 1b, removed 5

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  7eaa215

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• More files removed...

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  1ad3c1c

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• Resolve merge

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  cbcf76e

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• Minor changes to merge with latest changes

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  db6b9b8

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• Modified java_mem_gb to use select_first

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  e70ec78

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• Clean up CleanVcf.wdl inputs

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  2cb19ca

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• Forgot comma

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  0956b92

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• Forgot comma

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  48d81a8

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• Removed unnecessary params

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  f4112a2

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• Added runtime_override_clean_vcf_5

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  ad93a92

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Commits on Nov 4, 2024

• Minor changes

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  559a2ce

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Commits on Nov 12, 2024

• Merge branch 'main' into kj_sv_cleanvcf

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  df05435

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Commits on Nov 22, 2024

• Resolved merge conflicts

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  e197f0a

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Commits on Nov 24, 2024

• WIP

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  43db008

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Commits on Nov 25, 2024

• Initial preprocess script

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  e6e519d

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• Created postprocessing script

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  ccd5dde

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• Minor removal of > character

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  d60b01b

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• Python linting fixes

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  38eefb2

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Commits on Dec 5, 2024

• WIP - refactored WDLs to use new set of tools

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  be7f3bf

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Commits on Dec 6, 2024

• WIP

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  fec8d59

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Commits on Dec 11, 2024

• Updated pre/postprocess to use pipeline docker

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  e27026b

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Commits on Dec 12, 2024

• Finished testing cleanvcfpreprocess

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  a92904d

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• Undo header.txt addition

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  766acf6

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• Modified postprocess function, works now

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  05a17c2

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• Removed header.txt again

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  d403387

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Commits on Dec 13, 2024

• Updated header writing

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  170ec7c

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• Decommissioned post-process script

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  eed4c57

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• Updated vargq values

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  078155c

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Commits on Jan 6, 2025

• Minor update to pass correct VCF downstream

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  ffa4439

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• Created postprocessing file

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  c75c86a

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• Updated postprocessing order

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  0edef35

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• Updated header of output VCF to include all required fields

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  a2e7381

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Commits on Jan 7, 2025

• Updated changes pre-testing on gnomad

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  3aec8d0

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Commits on Jan 9, 2025

• Removed unnecessary runtime attributes

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  581c5c1

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Commits on Jan 13, 2025

• Added sex revisions for male GT

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  be3a801

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Commits on Jan 17, 2025

• Coalesced overlapping cnv tools into one

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  9a6da9d

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Commits on Jan 21, 2025

• Updated workflow inputs to reflect one-tool approach to overlapping CNVs

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  db4dfca

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Commits on Jan 22, 2025

• Resolved conflicts

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  9016dcb

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• Readded calcAF.wdl

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  24fc04e

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• Removed calcaf.wdl

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  c588ab1

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Commits on Jan 29, 2025

• Merge branch 'main' into kj_sv_cleanvcf

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  8a34292

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• Minor changes to make wdl more readable

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  a6588c6

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• Removed head from merge conflict

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  835f5b0

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