Github.com/vgteam/vg_wdl/giraffe_and_deeptrio

Core VG Giraffe mapping and DeepTrio calling workflow for maternal-paternal-child sample datasets. It takes as inputs reads in FASTQ and graphs containing the population-based haplotypes to genotype. The graphs files required include the XG, GCSA, GBWT, graph GBWT, Distance and Minimizer indexes. It outputs a VCF file and BAM file for the child along with optional RTG and hap.py vcf evaluation if the user provides benchmark truth-set VCFs.


This is a companion discussion topic for the original entry at github.com/vgteam/vg_wdl/giraffe_and_deeptrio