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arq5x / bedtools2

bedtools - the swiss army knife for genome arithmetic
MIT License
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Select sample from VCF #103

Closed chrismit closed 9 years ago

chrismit commented 10 years ago

The ability to select a sample by name to perform bed operations on. This would help with using vcf files from the 1000 genomes project where we are trying to intersect with certain individuals.

nkindlon commented 10 years ago

I think we should be able to do something like this, sure. Perhaps we could give an option or options that lets the user provide a name, list of names, or even a file of names. In the case of intersect, would these apply to the query, database, both, or should the user be able to specify this? I'll discuss this enhancement with Aaron at our lab meeting Monday. In the meantime, of course, you can filter results with grep and awk, though I realize this is slower and more cumbersome than having bedtools do it for you.

arq5x commented 9 years ago

This should be done with vcftools and then passed to bedtools.