Description

Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation

Input

name:type
description
pattern

meta{:bash}

:map

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

input{:bash}

:file

BAM/CRAM file

*.{bam,cram}

input_index{:bash}

:file

BAM/CRAI index file

*.{bai,crai}

target_bed{:bash}

:file

BED file containing target regions for variant calling

*.{bed}

target_bed_index{:bash}

:file

Index for BED file containing target regions for variant calling

*.{bed.tbi}

fasta{:bash}

:file

Genome reference FASTA file

*.{fa,fasta}

fai{:bash}

:file

Genome reference FASTA index file

*.{fa.fai,fasta.fai}

Output

name:type
description
pattern

vcf{:bash}

meta{:bash}

:map

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

*variants.vcf.gz{:bash}

:file

gzipped germline variant file

*.{vcf.gz}

vcf_tbi{:bash}

meta{:bash}

:map

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

*variants.vcf.gz.tbi{:bash}

:file

index file for the vcf file

*.vcf.gz.tbi

genome_vcf{:bash}

meta{:bash}

:map

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

*genome.vcf.gz{:bash}

:file

variant records and compressed non-variant blocks

*_genome.vcf.gz

genome_vcf_tbi{:bash}

meta{:bash}

:map

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

*genome.vcf.gz.tbi{:bash}

:file

index file for the genome_vcf file

*_genome.vcf.gz.tbi

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

included in
sarek
maintainer
Github user arontommi
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