Description

Identify chromosomal rearrangements.

Input

Name (Type)
Description
Pattern

meta (map)

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

]

input (file)

BAM/CRAM file

*.{bam,cram}

index (file)

BAM/CRAM index file

*.{bai,crai}

fasta (file)

Input FASTA file

*.{fasta,fa}

bwa_index (file)

BWA genome index files

Directory containing BWA index *.{amb,ann,bwt,pac,sa}

Output

Name (Type)
Description
Pattern

meta (map)

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

]

vcf (file)

vcf

*.{vcf}

ploidy (file)

tab

*.{ploidies.tab}

versions (file)

File containing software versions

versions.yml
included in
raredisease sarek
author
Github user maxulysse
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

sv
GPL-3.0-or-later

Search for structural variants.

github.com/SciLifeLab/TIDDIT github.com/SciLifeLab/TIDDIT/blob/master/README.md 10.12688/f1000research.11168.1