variantCalling - christianparobek/cambodiaWGS GitHub Wiki

As of December 2014, GATK's HaplotypeCaller is now the recommended genotyper - "no exceptions". So I'm modifying the alignment_pipeline.sh to use HaplotypeCaller now rather than UnifiedGenotyper. In this process, we have concerns about how GATK treats potentially mixed (MOI>1) samples. We think - but don't know - that it might see variant sites in mixed sites and throw those out because of having to many alleles there.