Description

SNP and Indel variant caller on a per-locus basis

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

]

intervals (file)

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

*.intervals

meta6 (map)

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

]

contamination (file)

Tab-separated file containing fraction of contamination in sequencing data (per sample) to aggressively remove

*

meta7 (map)

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

]

dbsnps (file)

VCF file containing known sites (optional)

*

meta8 (map)

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

]

comp (file)

Comparison VCF file (optional)

*

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

vcf (file)

VCF file containing called variants

*.vcf.gz

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.