Question

Looking For A Vcf/Bcf C++ Library

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11.5 years ago

Rlong ▴ 340

I am looking for a liberally licensed C++ library that can parse both VCF and BCF. I like vcflib, but it does not handle BCF. Suggestions?

vcf • 4.1k views

ADD COMMENT • link updated 11.5 years ago by pd3 ▴ 350 • written 11.5 years ago by Rlong ▴ 340

score 3 · Answer 1 · 2012-10-12

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11.5 years ago

pd3 ▴ 350

Try Heng's https://github.com/samtools/htslib

ADD COMMENT • link 11.5 years ago by pd3 ▴ 350

score 1 · Answer 2 · 2012-10-11

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11.5 years ago

Zev.Kronenberg 12k

If you can work in the SAM or BAM formats you can do a lot with the samtools header files.

http://samtools.sourceforge.net/samtools/masterTOC.shtml

On the same topic Bamtools also offers an API

https://github.com/pezmaster31/bamtools

Do you need to process the BCF?

ADD COMMENT • link 11.5 years ago by Zev.Kronenberg 12k

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Unfortunately, I can only be assured of having VCF/BCF files, and not necessarily the original aligned BAMs. I am working on a variant annotator, and I would like for it to able to take either VCF or BCF as input, and produce the same for output.

ADD REPLY • link 11.5 years ago by Rlong ▴ 340