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broadinstitute / gatk

Official code repository for GATK versions 4 and up
https://software.broadinstitute.org/gatk
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Add VCF input and support for allelic counts from indels to ModelSegments pipeline. #4903

Open samuelklee opened 6 years ago

samuelklee commented 6 years ago

Suggested by Peter Du, who observed that HaplotypeCaller finds ~3400 snps (~7700 snps + indels) in a mouse exome, vs. ~2000 hets found by CollectAllelicCounts + naive genotyping. See related issues #3915 and #4717.

samuelklee commented 5 years ago

I think this is still worth pursuing, but we need to do some legwork to set up good tests.

samuelklee commented 5 years ago

Also note that this is prototyped in the sl_ms_vcf branch.