Description

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

Input

Name (Type)
Description
Pattern

meta (map)

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

input (file)

BAM/CRAM file

*.{bam,cram}

input_index (file)

BAM/CRAI index file

*.{bai,crai}

fasta (file)

Genome reference FASTA file

*.{fa,fasta}

fai (file)

Genome reference FASTA index file

*.{fa.fai,fasta.fai}

target_bed (file)

BED file containing target regions for variant calling

*.{bed}

target_bed_index (file)

Index for BED file containing target regions for variant calling

*.{bed.tbi}

Output

Name (Type)
Description
Pattern

meta (map)

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

vcf (file)

gzipped germline variant file

*.{vcf.gz}

vcf_tbi (file)

index file for the vcf file

*.vcf.gz.tbi

genome_vcf (file)

variant records and compressed non-variant blocks

*_genome.vcf.gz

genome_vcf_tbi (file)

index file for the genome_vcf file

*_genome.vcf.gz.tbi

versions (file)

File containing software versions

versions.yml
included in
sarek
maintainer
Github user arontommi
get in touch
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Tools