Table 1.

Mutation caller parameters.

Caller	Parameters
MuTect 1.1.7	default (tumor_1od = 6.3 fraction_contamination = 0.02 normal_1od = 2.2 strand_artifact_lod = 2.0 strand_artifact_power_threshold = 0.9 dbsnp_normal_1od = 5.5 gap_events_threshold = 3 fraction_mapq_threshold = 0.5 pir_median_threshold = 10.0 pir_mad_threshold = 3.0 required_maximum_alt_allele_mapping_quality_score = 20 max_alt_alleles_in_normal_count = 2 max_alt_allele_in_normal_fraction = 0.03)
SomaticSniper 1.0.5.0	-Q 40 -L -G
VarScan 2.3.9	somatic –min-coverage 10 –min-coverage-normal 10 –min-coverage-tumor 10 –min-var-freq 0.05