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How are supplementary alignments handled by HaplotypeCaller?

sp580sp580 GermanyMember


I am curious about how HaplotypeCallers deals with secondary alignments. I know (based on the documentation and my own runs) that the filter NotSecondaryAlignmentReadFilter is applied but I do not see the filter NotSupplementaryAlignmentReadFilter (is it obsolete?, redundant?, hast it been renamed or merged with another filter maybe?)

Thanks in advance!

Best Answer


  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin

    I believe that HaplotypeCaller filters out secondary alignments and only uniquely mapped reads are used for variant discovery. The NotSupplementaryAlignmentReadFilter is still present in GATK4 documentation with the same name. Please let us know if this is the information you were looking for!

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