building a consensus FASTA from BAM(s)

[adaptivegenome]

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?

[andreagmu]

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

[andreagmu]

Or anyone else.. Thanks!

[peromhc]

see http://samtools.sourceforge.net/mpileup.shtml

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