Read mapping and SV genotyping using vg. It takes a CRAM file and graphs containing the structural variants to genotype. The XG and GCSA 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 mapping jobs. It also makes them short enough that they can be run on cheaper i
This is a companion discussion topic for the original entry at github.com/vgteam/vg_wdl/vg_map_call_sv_cram