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knausb / vcfR

Tools to work with variant call format files
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Support for bcf files #143

Closed explodecomputer closed 5 years ago

explodecomputer commented 5 years ago

Thanks for a very useful package. Do you have plans to allow vcfR to read bcf files? If not do you know of any that will?

knausb commented 5 years ago

I do not know of any R packages that will read BCF files. At some point I think I benchmarked BCF and the gzipped VCF and decided they performed very similarly. I would like to incorporate htslib into vcfR. #124 and #125 request this. However, I have yet to learn how to actually do this, and have not found a lot of time to code lately. So these have not been a high priority.

explodecomputer commented 5 years ago

Thanks for the fast reply! I did a bit of research and it seems that VariantAnnotation will, though some of its functionality seems to break (e.g. reading just regions).