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}

target_bed (file)

An optional bed file

*.{bed}

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