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arq5x / gemini

a lightweight db framework for exploring genetic variation.
http://gemini.readthedocs.org
MIT License
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Add aaf() option to --gt-filter #651

Open arq5x opened 8 years ago

arq5x commented 8 years ago

It would be nice to have the ability to filter variants based on the alternate allele frequency in specific subsets of individuals. Currently, we can filter based on the counts of specific genotypes, but aaf would be more generalizable.

For example:

(phenotype==2).(aaf < 0.01)
brentp commented 8 years ago

584 would enable this.

arq5x commented 8 years ago

Isn't that for the allele frequency in a single sample? What I meant to articulate was filtering based on the genotyped AF across all individuals meeting a specific phenotype.