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

]

bam (file)

Single input BAM file.

*.bam

bai (file)

The BAI file for the input BAM file

*.bai

read_group_setting (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

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

bam (file)

A BAM file with suffix_mergedReads.bam

*_mergedReads.bam

filelist (file)

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

*.txt.gz
author
Github user merszym
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

atlas
GPL v3

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

bitbucket.org/wegmannlab/atlas/wiki https://bitbucket.org/wegmannlab/atlas 10.1101/105346