Description

Estimate the post-mortem damage patterns of DNA

Input

Name (Type)
Description
Pattern

meta (map)

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

]

bam (file)

Single input BAM file

*.bam

bai (file)

The BAI file for the input BAM file

*.bai

fasta (file)

The reference genome provided as FASTA file

*.fasta

fai (file)

The FAI file for the reference genome FASTA file

*.fai

pool_rg_txt (file)

Optional. Provide the names of read groups that should be merged for PMD estimation.
All read groups that should be pooled listed on one line, separated by any white space.
Other read groups will be recalibrated separately.

*.txt

Output

Name (Type)
Description
Pattern

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

empiric (file)

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

*_PMD_input_Empiric.txt

exponential (file)

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

*_PMD_input_Exponential.txt

counts (file)

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

*_PMD_Table_counts.txt

table (file)

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

*_PMD_Table.txt

Tools

atlas
GPL v3

ATLAS, a suite of methods to accurately genotype and estimate genetic diversity