Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
bam:file
Single input BAM file
*.bam
bai:file
The BAI file for the input BAM file
*.bai
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
fasta:file
The reference genome provided as FASTA file
*.fasta
fai:file
The FAI file for the reference genome FASTA file
*.fai
Output
name:type
description
pattern
empiric
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*_PMD_input_Empiric.txt:file
A list of pmd patterns estimated with the empirical method for each readgroup
*_PMD_input_Empiric.txt
exponential
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*_PMD_input_Exponential.txt:file
A list of pmd patterns estimated with the exponential method for each readgroup
*_PMD_input_Exponential.txt
counts
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*_PMD_Table_counts.txt: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
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*_PMD_Table.txt: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
versions
versions.yml:file
File containing software versions
versions.yml
Tools
atlas
GPL v3
ATLAS, a suite of methods to accurately genotype and estimate genetic diversity
