Read mapping and SV genotyping using vg. This workflow uses the new and faster mapper (giraffe/gaffe). It takes a CRAM file and graphs containing the structural variants to genotype. The XG, minimizer and distance graph indexes as required, as well as the original VCF used to create the graph. Including the snarls index is optional but speeds up the computation. It outputs a VCF file. The CRAM files are converted to FASTQ in chunks. This is used to parallelize the CRAM conversion jobs and the ma
This is a companion discussion topic for the original entry at github.com/vgteam/vg_wdl/vg_mapgaffe_call_sv_cram