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Multisamples Snp Calling Within A Given Area

Hi, This link

gives us the command how to do multisamples calling SNPS. What I want is to call snp within a particular region such as chr8:100000-200000 etc.

Then what is the command? Thanks.

samtools bcftools snp sequence
• 2,575 views • link
updated by Pierre Lindenbaum 17K • | written by Zhshqzyc 53

1 answer

See the manual page for mpileup and the -r option 

(...)
-r STR  Only generate pileup in region STR
(...)

e.g:

samtools mpileup -C50 -gf ref.fasta -r chr3:1,000-2,000 in1.bam in2.bam
• 1 views • link
written by Pierre Lindenbaum 17K

And the -l option if you have many regions....

• 0 views • link
written by Sean Davis 2.7K

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