I am wondering how HaplotypeCaller in GATK 3.1 handles multimappers? I thought I read that they are passed over for variant calling but stay in the realigned, recalibrated BAM for 'completions sake', like marking duplicates not removing them but cannot find supporting info on the website or from farther afield,
Presumably it is the NotPrimaryAlignmentFilter but there is no info on that posted yet. I know I can output a BAM from HC with haplotype info in there but can I just get reads used in variant calls? Or should I trim the BAM myself to retain reads I want used? I do this for mark duplicates (removed) but for multimappers I would like to know how you define so I can do the same. The reason is for coverage estimates, using bamtobed or such means I take all realigned, recalibrated which is many more lines including multimappers which skews my results.