Description

Splits reads that contain Ns in their cigar string

Input

Name (Type)
Description
Pattern

meta (map)

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

bam (list)

BAM/SAM/CRAM file containing reads

*.{bam,sam,cram}

bai (list)

BAI/SAI/CRAI index file (optional)

*.{bai,sai,crai}

intervals (file)

Bed file with the genomic regions included in the library (optional)

meta2 (map)

Groovy Map containing reference information
e.g. [ id:‘reference’ ]

fasta (file)

The reference fasta file

*.fasta

meta3 (map)

Groovy Map containing reference information
e.g. [ id:‘reference’ ]

fai (file)

Index of reference fasta file

*.fasta.fai

meta4 (map)

Groovy Map containing reference information
e.g. [ id:‘reference’ ]

dict (file)

GATK sequence dictionary

*.dict

Output

Name (Type)
Description
Pattern

bam (file)

Output file with split reads (BAM/SAM/CRAM)

*.{bam,sam,cram}

versions (file)

File containing software versions

versions.yml
included in
rnadnavar rnavar
maintainer
Github user kevinmenden
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

gatk4
Apache-2.0

Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.

gatk.broadinstitute.org/hc/en-us gatk.broadinstitute.org/hc/en-us/categories/360002369672s 10.1158/1538-7445.AM2017-3590