I am analyzing WGS data with vg, following the recommendation made on the vgTeam GitHub wiki page ("Working with a whole genome variation graph" and "Whole-genome calling and genotyping"), and I am unsure what to do about the issue of duplicate reads. Does vg take care of this in the commands recommended in the above pages? or is there another vg tool I should be using on the GAMs prior to variant calling?
Thanks in advance.
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written
by
lhomas •
1 answer
This is a great question. There is indeed no vg tool yet to mark duplicates. The only workaround, which isn't great, is to use a BAM file to detect duplicates. Please make a feature request on github! We are working on some changes to replace GAM as a default format which should make it possible to write such a tool more efficiently soon,.
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