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  • 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

  • #2
    Hi adaptivegenome. Could you help me out with building a consensus FASTA from a single BAM file? Thank you.

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    • #3
      Or anyone else.. Thanks!

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      • #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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