Fetching All Alignments From A Sam/Bam By Read Header In Perl

Question

[Abhi]

Hey Guys

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.

Thanks!
-Abhi

Answer 1

[SES]

Have a look at Bio::DB::Sam. This does not ship with the core BioPerl, and to compile this you will need to get the Kent source tree a recent version of SAMtools. Building this can be tricky depending on your OS, but I'm sure there are plenty of people that can offer advice.

[Chris Fields]

Actually, you don't need the Kent source tree (that would be needed for Bio::DB::BigFile), but you do need a recent version of samtools

[SES]

Thanks, Chris. That was my error in memory. It looks like Bio::DB::BigFile is for BigWig and BigBed anyway, so at least Bio::DB::Sam is appropriate for the original question.

[Abhi]

@SES @Chris : Thanks guys .. on my weekend test list

[Chris Fields]

Actually, you don't need the Kent source tree (that would be Bio::DB::BigFile), but you do need a recent version of samtools.