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Which BAM to give FilterAlignmentArtifacts

Hello,

In the GATK4 somatic SNVs+Indels best practices WDL, the BAM file given to FilterAlignmentArtifacts is the same tumor BAM as given to Mutect2. However, in the FilterAlignmentArtifacts documentation is says that the input bam should be the reassembly bamout produced by Mutect2. Further, the Mutect2 documentation for the --bam-output argument says that it is only really used for debugging.

I'm just wondering which BAM file I should provide to FilterAlignmentArtifacts?

Thanks!
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Answers

  • bshifawbshifaw Member, Broadie, Moderator admin

    "The original bam will also work but might fail to filter some indels." but i'll confirm with dev team next week if this is intentional or if the documentations needs an update.

    You can probably use either or depending on how sensitive you want to be with filtering indels. Use the bamout for the tool to properly filter out indels or original bam if your focus is on SNP and not too concerned with having a few extra Indel artifacts. Keep in mind the tool is marked as EXPERIMENTAL.

  • bshifawbshifaw Member, Broadie, Moderator admin
    Accepted Answer

    @dt7 ,

    Just confirmed, the original bam is what should be used and not the bamout. The tool doc will need to be updated.

    Thanks for finding the discrepancy.

  • dt7dt7 Member
    Great, thanks for the clarification!
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