building a consensus FASTA from BAM(s)

adaptivegenome

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#1

building a consensus FASTA from BAM(s)

11-30-2011, 03:29 PM

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
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andreagmu

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#2

06-10-2013, 03:57 PM

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

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#3

06-10-2013, 04:01 PM

Or anyone else.. Thanks!
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peromhc

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#4

06-18-2013, 07:10 PM

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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