SEQanswers - View Single Post - Fastest way to extract differing positions from each alignment in a BAM file

CHRYSES · 12-14-2011, 06:47 AM

Hi,

What would be the fastest way (I have to do this hundreds of millions times) to extract for each aligned read in a BAM file:
1) The positions where the read bases differ from a reference sequence.
2) The PHRED base quality values of these bases. If the difference is an indel, the quality value will, of course, be skipped.

As far as I know, I cannot use mpileup or anything I know of due to memory limitation as this is a very custom amplicon reference analysis, with >500 million coverage per base position on the reference amplicon.

In short, I need to apply an efficient approach to extract all differing positions for each aligned read.

Thanks.

12-14-2011, 06:47 AM	#1
CHRYSES Member Location: Netherlands Join Date: Dec 2009 Posts: 13	Fastest way to extract differing positions from each alignment in a BAM file Hi, What would be the fastest way (I have to do this hundreds of millions times) to extract for each aligned read in a BAM file: 1) The positions where the read bases differ from a reference sequence. 2) The PHRED base quality values of these bases. If the difference is an indel, the quality value will, of course, be skipped. As far as I know, I cannot use mpileup or anything I know of due to memory limitation as this is a very custom amplicon reference analysis, with >500 million coverage per base position on the reference amplicon. In short, I need to apply an efficient approach to extract all differing positions for each aligned read. Thanks. Last edited by CHRYSES; 12-14-2011 at 06:52 AM.