Description

Generates a list of locations that should be considered for local realignment prior genotyping.

Input

Name (Type)
Description
Pattern

meta (map)

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

]

bam (file)

Sorted and indexed BAM/CRAM/SAM file

*.bam

bai (file)

BAM index file

*.bai

meta2 (map)

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

]

fasta (file)

Reference file used to generate BAM file

.{fasta,fa,fna}

meta3 (map)

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

]

fai (file)

Index of reference file used to generate BAM file

.fai

meta4 (map)

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

]

dict (file)

GATK dict file for reference

.dict

meta5 (map)

Groovy Map containing file meta-information for known_vcf.
e.g. [ id:‘test’, single_end

]

known_vcf (file)

Optional input VCF file(s) with known indels

.vcf

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

intervals (file)

File containg intervals that represent sites of extant and potential indels.

*.intervals
author
Github user jfy133
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Tools

gatk
https://software.broadinstitute.org/gatk/download/licensing', 'BSD', 'https://www.broadinstitute.org/gatk/about/#licensing

The full Genome Analysis Toolkit (GATK) framework, license restricted.

gatk.broadinstitute.org/hc/en-us github.com/broadinstitute/gatk-docs