modules/atlas_pmd

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

File containing software versions

A list of pmd patterns estimated with the empirical method for each readgroup

A list of pmd patterns estimated with the exponential method for each readgroup

The counts of all possible transitions for each read position
(or up to a certain position, see specific command length)

For all possible transitions the ratio of the transition counts,
which are taken from the _counts.txt table, over the total amount
of the base that was mutated, for each position and readgroup