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How are supplementary alignments handled by HaplotypeCaller?
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!