Description

split single end read groups by length and merge paired end reads

Input

name:type
description
pattern

meta:map

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

read_group_settings:file

TXT file containing the split and merge settings for each readgroup. Each line consist of one readgroup, single/double identifier and the maximum cycle number of the sequencer. e.g. “RG1 single 100”

*.txt

blacklist:file

blacklist.txt (optional), A txt file with blacklisted read names that should be ignored and just written to file, each on a new line

*.txt

Output

name:type
description
pattern

bam

meta:map

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

*_mergedReads.bam:file

A BAM file with suffix_mergedReads.bam

*_mergedReads.bam

txt

meta:map

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

*.txt.gz:file

A file listing all reads that were filtered out in the merging process with suffix_ignoredReads.txt.gz

*.txt.gz

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