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  • 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, 02:10 PM.

  • #2
    The samtools mpileup method that you found should work just fine.

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    • #3
      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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