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szpiech / selscan

Haplotype based scans for selection
GNU General Public License v3.0
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Support for VCF files #9

Closed tomkinsc closed 9 years ago

tomkinsc commented 9 years ago

It would be helpful to have direct support for VCF files, with tabix indices

szpiech commented 9 years ago

I've included basic VCF support (without tabix) in the latest commit 7af301ded3fc8a23631bda239c925f52ee8c3f0d.

Tabix support may have to wait a bit, but I hope this is satisfactory in the meantime.

tomkinsc commented 9 years ago

This is terrific. Thanks, Zachary! I'll likely need to do some pre-filtering on the VCF files I have, but at least this way I can drop records rather than reform all of the data to tped format.

One question: How does selscan handle VCF records with multi-allelic variants? (As are found for SNPs in the phase 3 1000 Genomes dataset, for example.)

On May 6, 2015, at 16:13, Zachary A Szpiech notifications@github.com wrote:

I've included basic VCF support (without tabix) in the latest commit 7af301d.

Tabix support may have to wait a bit, but I hope this is satisfactory in the meantime.

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