Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.

Emitting ref vs. alt allele counts on all sites

eranmickeranmick Posts: 1Member


I would like to use UnifiedGenotyper to produce a vcf file where all sites I specify via BED file will have a count of reads carrying the reference allele and a count of reads carrying an alternate allele, regardless of whether a variant has been called in the site.
I've tried to use EMIT_ALL_SITES, but this appears not to provide this count breakdown for sites that are not called as variable.
I would appreciate any pointers. I am using GATK 2.2.4.

Thank you very much.

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