FilterAlignmentArtifacts - only emitting PASS variants
Answered
Hi,
FilterAlignmentArtifacts only emits PASS variants. Is this expected behavior? I would expect it would just add 'alignment' filter and output all variants. Otherwise it prevents users from fine-tuning their final filtering.
Does the "--dont-skip-filtered-variants" fix this?
-
Hi GE, please give more information regarding the behavior that you observed so that we can look into it.
-
Hi,
This is the recommended best practices Mutect2 pipeline from Terra:
The unexpected behavior I found was that the output of FilterMutectCalls contains PASS and all non-PASS variants, but the output of FilterAlignmentArtifacts only processes and outputs variants that are PASS from the input VCF. The result of FilterAlignmentArtifacts then contains PASS variants that PASSed FilterMutectCalls and FilterAlignmentArtifacts, and variants labeled with the 'alignment' filter that PASSed FilterMutectCalls but not FilterAlignmentArtifacts. But the output of FilterAlignmentArtifacts does not contain variants that are not PASS after FilterMutectCalls.
This is unexpected behavior because in general, filtering tools should simply add FILTER labels to variants, but keep all variants. They should not completely remove filtered variants. Regardless, this behavior is not documented in FilterAlignmentArtifacts.
-
Hi GE,
It looks like this is expected behavior for this tool. The default behavior of the tool is only using the PASS variants because it is reassembling all of the alt supporting reads at these sites. It could take quite a bit more time to include the non-PASS variants, which is why that is not default. If you want to include the non-PASS variants, use the --dont-skip-filtered-variants argument, as you wrote above.
You can read more regarding this tool in the Mutect whitepaper on page 13, section 3C: https://github.com/broadinstitute/gatk/blob/master/docs/mutect/mutect.pdf
Best,
Genevieve
Please sign in to leave a comment.
3 comments