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Header is missing description for FILTER-PASS #6426

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npatel22526 opened this issue Jan 29, 2020 · 0 comments · Fixed by #6436
Closed
1 task

Header is missing description for FILTER-PASS #6426

npatel22526 opened this issue Jan 29, 2020 · 0 comments · Fixed by #6436
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@ldgauthier

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@npatel22526
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Bug Report

Affected tool(s) or class(es)

FilterMutectCalls

Affected version(s)

  • Latest public release version [4.1.4.1]

Description

Header is missing description for "##FILTER=<ID=PASS" , it causes inaccurate parsing of VCF

Steps to reproduce

Run the FilterMutectCalls on any mutect2 VCF available

Thanks,
Nick
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@ldgauthier ldgauthier

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Add "PASS" filter line for ApplyVQSR and FilterMutectCalls broadinstitute/gatk
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@ldgauthier @davidbenjamin @npatel22526