Update on genotyping option?

Illumina / manta

Structural variant and indel caller for mapped sequencing data

GNU General Public License v3.0

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Update on genotyping option? #247

Open katherinef opened 3 years ago

katherinef commented 3 years ago

Hello,

I know this has been requested before, but are there any immediate plans to implement an option to genotype a list of variants supplied in an input VCF (similar to the forcedGT option in Strelka2). I am working with a large cohort and would like to call SVs in a subset and then genotype these SVs across the full cohort.

Many thanks,

Kath

jjfarrell commented 3 years ago

I am also interested in this feature for genotyping across a cohort of 5k samples.

biozzq commented 3 years ago

Hi I think you can try GenomeSTRiP/Paragraph/graphtyper.