Common mutations in cancer that will be genotyped and passed through into the merged VCF if they have even low-level evidence of a mutation (by default, marked with filter DOCM_ONLY)

roi_intervals is a list of regions (in interval_list format) within which to call somatic variants

scatters each supported variant detector (varscan, pindel, mutect) into this many parallel jobs

An optional VCF with variants that will be flagged as 'VALIDATED' if found in this pipeline's main output VCF

ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus

ensembl version - Must be present in the cache directory. Example: 95

Determines whether variants found only via genotyping of DOCM sites will be filtered (as DOCM_ONLY) or passed through as variant calls

genome assembly to use in vep. Examples: GRCh38 or GRCm38

custom type, check types directory for input format

Sets the stringency (log-likelihood ratio) used to filter out non-somatic variants. Typical values are 10=high stringency, 5=normal, 3=low stringency. Low stringency may be desirable when read depths are low (as in WGS) or when tumor samples are impure.

Sets the purity of the tumor used in the somatic llr filter, used to remove non-somatic variants. Probably only needs to be adjusted for low-purity (< 50%). Range is 0 to 1

Sets the fraction of tumor present in the normal sample (range 0 to 1), used in the somatic llr filter. Useful for heavily contaminated adjacent normals. Range is 0 to 1