Description

Estimates the numbers of unique molecules in a sequencing library.

Input

Name (Type)
Description
Pattern

meta (map)

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

]

input (file)

BAM/CRAM/SAM file

*.{bam,cram,sam}

fasta (file)

The reference fasta file

*.fasta

fai (file)

Index of reference fasta file

fasta.fai

dict (file)

GATK sequence dictionary

*.dict

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

metrics (file)

File containing metrics on the input files

*.{metrics}
included in
rnadnavar sarek
authors
Github user FriederikeHanssen Github user maxulysse
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

gatk4
Apache-2.0

Genome Analysis Toolkit (GATK4)

gatk.broadinstitute.org/hc/en-us https://github.com/broadinstitute/gatk 10.1158/1538-7445.AM2017-3590