Question: How do I deal with duplicate reads when using vg to analyse WGS data?
0
gravatar for lhomas
4 months ago by
lhomas0
lhomas0 wrote:

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.

vg • 144 views
ADD COMMENTlink modified 4 months ago by glenn.hickey140 • written 4 months ago by lhomas0
0
gravatar for glenn.hickey
4 months ago by
glenn.hickey140
glenn.hickey140 wrote:

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,.

ADD COMMENTlink written 4 months ago by glenn.hickey140
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1017 users visited in the last hour