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vatlab / varianttools

software tool for the manipulation, annotation, selection, and analysis of variants in the context of next-gen sequencing analysis
https://vatlab.github.io/vat-docs/
GNU General Public License v3.0
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How to show samples with heterogyzous genotype? #102

Closed mullinyu closed 5 years ago

mullinyu commented 5 years ago

I can do the following to list the samples having that allele. But, how can I if I would like to list those samples with heterogyzous genotype (wildtype and alternate)?

vtools select variant 'chr="3" AND pos=14187449 AND ref="G" AND alt="T"'-o chr pos ref alt dbSNP.name "samples()"

Thanks!

BoPeng commented 5 years ago

DId you try

samples('geno_filter=GT=1')

as described here?

mullinyu commented 5 years ago

Thanks! It works perfectly!!! Sorry I didn't read that page.