Question: can HipSTR output confident reference calls?

tfwillems / HipSTR

Genotype and phase short tandem repeats using Illumina whole-genome sequencing data

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Question: can HipSTR output confident reference calls? #28

Closed nh13 closed 7 years ago

nh13 commented 7 years ago

If the samples HipStr is joint calling all match the reference, is a variant record/line outputted. In many cases, it is important not only to see the variant sites, but also evidence for non-variant sites (think gVCFs).

tfwillems commented 7 years ago

Yes. If HipSTR genotypes an STR and no variants are detected across any of the samples, it'll automatically output a VCF record with no alternate alleles in which all samples have a 0/0 genotype.