Advanced Parameters

Advanced Parameters

Some advanced CaVEMan parameters are available via cgpCaVEManWrapper. This page explains each one and their effects on CaVEMan analysis.

Prior Somatic Probability

-prior-mut-probability

Increasing this value will increase the likelihood of a mutation being called at any position. Increasing this may be useful where sensitivity is preferred to specificity such as clinical detection or when running targetted mutation discovery.

Prior germline mutant probability

-prior-snp-probability

Increasing this value increases the likelihood of a position being called as a germline (SNP) mutation. Decreasing this value can help rescue variants called as SNPs due to low coverage.

Mutation output cutoff

-mut_probability_cutoff

The minimum sum probability of all possible somatic mutation genotypes before a position is output to the muts.vcf file. Increasing this value will reduce the number of mutations output to the file.

Germline output cutoff

-snp_probability_cutoff

The minimum sum probability of all possible germline mutation (SNP) genotypes before a position is output to the snp.vcf file. Increasing this value will reduce the number of SNPs output.