Why do default read filters differ between tools used in GATK Best Practices Workflows?
Answered
Dear GATK Team,
I understand that with many GATK tools, default Read filters are applied. However, these differ between tools and therefore, differ between steps of Best Practices Workflows, such as between Mutect2 and GetPileupSummaries as part of the Somatic short variant discovery (SNVs + Indels).
When using tools in one workflow, such as the Somatic short variant discovery (SNVs + Indels), why are read filters not all applied from the outset or kept the same throughout the workflow?
Thank you for your time and help.
Kind regards.
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Hi,
Can you please elaborate with some specifics? I can see that resource files listed for some parameter values are vague and don't match what's in the resource bundle. I'll look into getting that revised. Ideally, https://gatk.broadinstitute.org/hc/en-us/articles/360035894731 would include the exact commands at each section with specific reference to resource bundle files. Would that address your issue?
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Thank you for your reply Brian Haas.
I am referring to default read filters, such as those below.
Mutect2
- NonChimericOriginalAlignmentReadFilter
- NotSecondaryAlignmentReadFilter
- GoodCigarReadFilter
- NonZeroReferenceLengthAlignmentReadFilter
- PassesVendorQualityCheckReadFilter
- ReadLengthReadFilter
- MappedReadFilter
- MappingQualityAvailableReadFilter
- NotDuplicateReadFilter
- MappingQualityReadFilter
- MappingQualityNotZeroReadFilter
- WellformedReadFilter
GetPileupSummaries
- GoodCigarReadFilter
- NonZeroReferenceLengthAlignmentReadFilter
- PassesVendorQualityCheckReadFilter
- MappedReadFilter
- MappingQualityAvailableReadFilter
- NotDuplicateReadFilter
- PrimaryLineReadFilter
- MateOnSameContigOrNoMappedMateReadFilter
- MappingQualityNotZeroReadFilter
- WellformedReadFilter
Why not apply all read filters that will be used in various GATK tools in the Best Practices workflow in the first step (e.g. Mutect2 in Somatic short variant discovery (SNVs + Indels)), rather than adding further filters in later steps?
Thank you for your help.
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Hi ISmolicz,
The GATK support team is focused on resolving questions about GATK tool-specific errors and abnormal results from the tools. For all other questions, such as this one, we are building a backlog to work through when we have the capacity.
Please continue to post your questions because we will be mining them for improvements to documentation, resources, and tools.
We cannot guarantee a reply, however, we ask other community members to help out if you know the answer.
For context, check out our support policy.
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I suspect the read filters are intended to be consistent, and if there are differences it was likely an oversight. Mark Fleharty is the authority here and might comment further.
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Thank you for your reply Brian Haas. It would be useful if fleharty could comment to clarify further but I understand if other questions posted on the GATK Forum are priority.
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