Description

Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation in small cohorts and somatic variation in tumor/normal sample pairs

Input

Name (Type)
Description
Pattern

meta (map)

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

]

input_normal (file)

BAM/CRAM/SAM file

*.{bam,cram,sam}

input_index_normal (file)

BAM/CRAM/SAM index file

*.{bai,crai,sai}

input_tumor (file)

BAM/CRAM/SAM file

*.{bam,cram,sam}

input_index_tumor (file)

BAM/CRAM/SAM index file

*.{bai,crai,sai}

manta_candidate_small_indels (file)

VCF.gz file

*.{vcf.gz}

manta_candidate_small_indels_tbi (file)

VCF.gz index file

*.tbi

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_tbi (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’, single_end

]

vcf_indels (file)

Gzipped VCF file containing variants

*.{vcf.gz}

vcf_indels_tbi (file)

Index for gzipped VCF file containing variants

*.{vcf.gz.tbi}

vcf_snvs (file)

Gzipped VCF file containing variants

*.{vcf.gz}

vcf_snvs_tbi (file)

Index for gzipped VCF file containing variants

*.{vcf.gz.tbi}

versions (file)

File containing software versions

versions.yml