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

Abhishek Pratap abhishek.vit at gmail.com
Thu Feb 23 19:55:02 EST 2012


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.

PS:  I also posted this earlier on Biostar.

Thanks!
-Abhi


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