Custom Mutation Rate Regions with a BED File

In addition to targeting certain regions, you can use a BED file with a custom field entered in any column after the third.

mutation_regions: /path/to/mutation_regions.bed

The text pattern is “mut_rate=0.0001” followed by a delimiter (end of line, space, semicolon, comma, bar) where the number after the equal sign is any float, and will be the mutation rate for the region defined in columns 1-3.

chr1    39930   39957   Bed_info    mut_rate=0.002
chr2    0   111199  Other_bed_info  mut_rate=0.02

Any region outside of the regions defined in the mutation regions BED will be assigned the default mutation rate, set by the mutation model, which can be overridden a custom default defined in the config file. For example, if you only want to have mutations in exomes, but you want reads from the full genome, you could set the mutation_rate to 0.0 and use a bed file defining all exomes, with a column appende mut_rate=0.0011 or whatever mutation rate you desire. This BED works in conjunction with the target_bed, and any region outside the target bed will be excluded from reads anyway, and thus will have no variants.