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

]

dbsnp: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

vcf

meta:map

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

]

*.vcf.gz:file

VCF file containing called variants

*.vcf.gz

versions

versions.yml:file

File containing software versions

versions.yml

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.