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  • slny
    Member
    • Mar 2011
    • 54
    #1

    How to get consensus sequence from .sam file?

    I'm trying to get consensus sequence from sam file according to the instruction from samtools website as below.

    samtools pileup -cf ref.fa aln.bam | samtools.pl pileup2fq -D100 > cns.fastq

    However, there is actually no samtools.pl. Is there any way I could get the consensus sequence from sam file?

    Thanks
    Tags: None
  • swbarnes2
    Senior Member
    • May 2008
    • 910
    #2
    In the latest release, its in the misc folder. And I think the latest release has a vcf2fq subroutine in vcfutils, but it's slow because you have to make a massive all-points .bcf file, and neither program will correct for indels.

    Comment

    • slny
      Member
      • Mar 2011
      • 54
      #3
      Yes, I found samtools.pl in misc folder. Thanks.

      Comment

      • dagarfield
        Member
        • Aug 2010
        • 39
        #4
        I think you may find this link helpful
        Multisample SNP Calling
        http://samtools.sourceforge.net/mpileup.shtml


        Pileup is now depreciated.

        Comment

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