And the -l option if you have many regions....
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Sean Davis
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.
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Pierre Lindenbaum
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Zhshqzyc •
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Zhshqzyc •
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
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