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  • srividya
    Junior Member
    • Sep 2010
    • 6
    #1

    Samtools pileup Consensus with 0.1.12a version

    Hello,

    I am using samtools 0.1.12a version for pileup consensus variant calling (-vc). I have aligned the reads with Soap Aligner and I am trying to call the consensus SNPs. Though, the pileup(only -f option) for the bam file is getting generated, I am unable to generate the consensus (-vc option) with it. I checked the CIGAR and also the sam file. They are pretty much looking normal. Can anyone tell what might be the problem?

    Thanks,
    Srividya
    Tags: None
    • nilshomer
      Nils Homer
      • Nov 2008
      • 1283
      #2
      Post a small set of reads that give this problem. Also, consider moving to the latest version of samtools, which uses "mpileup" instead of "pileup".

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