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Old 12-14-2011, 06:47 AM   #1
CHRYSES
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Location: Netherlands

Join Date: Dec 2009
Posts: 13
Default 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.
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