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  • adaptivegenome
    Super Moderator
    • Nov 2009
    • 436
    #1

    building a consensus FASTA from BAM(s)

    Building a FASTA consensus sequence from a single BAM file is straightforward. However, if I had several BAM files representing a number of genomes in a population, and I wanted to build a single consensus of all of these BAM files, would I simply get the consensus of all the reads in all the BAMs for each position?

    Also, how are positions where equal numbers of reads support a different base resolved?
    Last edited by adaptivegenome; 11-30-2011, 03:31 PM. Reason: typo
    Tags: None
  • andreagmu
    Junior Member
    • Jun 2013
    • 2
    #2
    Hi adaptivegenome. Could you help me out with building a consensus FASTA from a single BAM file? Thank you.

    Comment

    • andreagmu
      Junior Member
      • Jun 2013
      • 2
      #3
      Or anyone else.. Thanks!

      Comment

      • peromhc
        Senior Member
        • Sep 2009
        • 108
        #4
        see http://samtools.sourceforge.net/mpileup.shtml

        Code:
        samtools mpileup -uf ref.fa aln.bam | bcftools view -cg - | vcfutils.pl vcf2fq > cns.fq

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