SEQanswers - View Single Post - Question of retrieving nucleotides from a list of genomic coordinates..

westerman · 09-13-2012, 07:12 AM

Since a BAM should contain overlapping reads that may or may not agree at any particular base instead of a single sequence then the answer to your question is not straight-forward. First you'll need to generate a consensus sequence via 'samtools', 'bcftools' and 'vcfutils' ... see: http://samtools.sourceforge.net/mpileup.shtml. Having gotten that then you can pull out the bases.

There may be easier ways but that is how I would do it.

09-13-2012, 07:12 AM	#6
westerman Rick Westerman Location: Purdue University, Indiana, USA Join Date: Jun 2008 Posts: 1,104	Since a BAM should contain overlapping reads that may or may not agree at any particular base instead of a single sequence then the answer to your question is not straight-forward. First you'll need to generate a consensus sequence via 'samtools', 'bcftools' and 'vcfutils' ... see: http://samtools.sourceforge.net/mpileup.shtml. Having gotten that then you can pull out the bases. There may be easier ways but that is how I would do it.