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

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}

fasta:file

Genome reference FASTA file

*.{fa,fasta}

fai:file

Genome reference FASTA index file

*.{fa.fai,fasta.fai}

Output

name:type
description
pattern

vcf_indels

meta:map

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

]

*.somatic_indels.vcf.gz:file

Gzipped VCF file containing variants

*.{vcf.gz}

vcf_indels_tbi

meta:map

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

]

*.somatic_indels.vcf.gz.tbi:file

Index for gzipped VCF file containing variants

*.{vcf.gz.tbi}

vcf_snvs

meta:map

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

]

*.somatic_snvs.vcf.gz:file

Gzipped VCF file containing variants

*.{vcf.gz}

vcf_snvs_tbi

meta:map

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

]

*.somatic_snvs.vcf.gz.tbi:file

Index for gzipped VCF file containing variants

*.{vcf.gz.tbi}

versions

versions.yml:file

File containing software versions

versions.yml

Tools

included in
rnadnavar sarek
maintainer
Github user drpatelh
get in touch
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