default read filters in haplotypecaller in GATK

prasundutta87prasundutta87 EdinburghMember


Are these still the read filters applied in GATK haplotypecaller (gvcf mode)?-

• HCMappingQualityFilter (Default 20)
• MalformedReadFilter
• BadCigarFilter
• UnmappedReadFilter
• NotPrimaryAlignmentFilter
• FailsVendorQualityCheckFilter
• DuplicateReadFilter
• MappingQualityUnavailableFilter

I don't remember where I got it from, it must be some old gatk document. But, is it still valid for GATK4?

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