Extract genotype from hg19

Question

[DVA]

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.

Answer 1

[Chris Fields]

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.

[DVA]

Thanks Chris. I will give that a shot.