Multisamples Snp Calling Within A Given Area

Question

[Zhshqzyc]

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.

Answer 1

[Pierre Lindenbaum]

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

[Sean Davis]

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