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Old 04-29-2014, 02:06 PM   #1
Location: Auckland

Join Date: Sep 2011
Posts: 72
Default Looking at specific positions in a BAM file for SNPs

Hi, I have a bunch of BAM files of mapped RNAseq reads to the human genome.

I also have a list of known positions where SNPs may or may not be.

I was wondering if there is a fast way (preferably scriptable) to look at a particular position in a BAM/SAM file to see if there is a SNP there.

I understand that I can use samtools/mpileup to globally call variants. It's just that all I really want to do is look at specific positions.

Edit: to (possibly) answer my own question, samtools mpileup has these options..

-l FILE list of positions (chr pos) or regions (BED)
-r STR region in which pileup is generated [null]

will see if that works..

Last edited by danwiththeplan; 04-29-2014 at 02:10 PM.
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Old 04-29-2014, 02:16 PM   #2
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

The samtools mpileup method that you found should work just fine.
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Old 04-29-2014, 02:20 PM   #3
Location: Auckland

Join Date: Sep 2011
Posts: 72

Thanks, I have a bad habit of asking a question and answering it myself in about a minute, but I guess it helps people who are working on the same issue!
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bam, mpileup, samtools, snp, vcf

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