INCLUDE chr21 Variant Pipeline Development Project

This repo is used to house tools and workflows to improve and enhance analysis of non-diploid human genome data

Kids First DRC GATK HaplotypeCaller Modified Ploidy BETA Workflow

This is a research workflow for users wishing to modify the ploidy of certain regions of their existing GVCF calls. This uses the coalescent genotype model, equivalent to GATK 3.8 from Sentieon, a close analog of the original production workflow GATK 3.5 (via 4beta).

KFDRC Sentieon DNAscope/Haplotyper Hybrid Mixed Ploidy Workflow

This is a beta workflow to test the efficacy of using DNAscope + Haplotyper for mixed ploidy samples.