Question: Extract genotype from hg19
0
gravatar for DVA
3.6 years ago by
DVA530
United States
DVA530 wrote:

I have a large list of chr and positions, and would like to obtain the genotype of these positions in hg19. I saw this earlier post, but is there any easier way besides using samtools for each of the positions please?

Thank you.

hg19 • 1.0k views
ADD COMMENTlink modified 3.6 years ago by Chris Fields2.1k • written 3.6 years ago by DVA530
2
gravatar for Chris Fields
3.6 years ago by
Chris Fields2.1k
University of Illinois Urbana-Champaign
Chris Fields2.1k wrote:

seqtk has the 'subseq' command which has a bed option:

seqtk subseq [options] <in.fa> <in.bed>|<name.list>

This can generate tab-delim output as well using -t.

ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by Chris Fields2.1k

Thanks Chris. I will give that a shot.

ADD REPLYlink written 3.6 years ago by DVA530
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