Should we pass Omni to BQSR?

[jasonwalker80]

BQSR should not need the omni VCF. The omni VCF is a list of sites used by verifyBamId for identifying contamination (really mixing of multiple samples).

analysis-workflows/example_data/somatic_exome.yaml

Line 50 in 43c790e

- path: somatic_inputs/hla_and_brca_genes_omni.vcf.gz