[Bioperl-l] fetching all alignments from a sam/bam by read header in perl

Peter Cock p.j.a.cock at googlemail.com
Fri Feb 24 04:24:35 EST 2012


On Fri, Feb 24, 2012 at 12:55 AM, Abhishek Pratap
<abhishek.vit at gmail.com> wrote:
> I am wondering if there is a slick way access all the possible
> alignments for a read present in sam or bam file given the read
> header. Since the existing codebase is in perl I would prefer
> something which can be done in/via perl.
>
> By default BAM's are indexed by location so the inbuilt samtools
> indexing wont work I guess.
>
> I should also say the input bam file will have in the order of 500
> million total alignments and many reads are expected to be aligned to
> more than one place in the genome. Given the size of the data loading
> it all in one big hash is not turning out to be memory friendly.

Are you asking for SAM/BAM read lookup by read name?

> PS:  I also posted this earlier on Biostar.

Link?

Peter



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