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{:bash}

:map

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

input_normal{:bash}

:file

BAM/CRAM/SAM file

*.{bam,cram,sam}

input_index_normal{:bash}

:file

BAM/CRAM/SAM index file

*.{bai,crai,sai}

input_tumor{:bash}

:file

BAM/CRAM/SAM file

*.{bam,cram,sam}

input_index_tumor{:bash}

:file

BAM/CRAM/SAM index file

*.{bai,crai,sai}

manta_candidate_small_indels{:bash}

:file

VCF.gz file

*.{vcf.gz}

manta_candidate_small_indels_tbi{:bash}

:file

VCF.gz index file

*.tbi

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_indels{:bash}

meta{:bash}

:map

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

*.somatic_indels.vcf.gz{:bash}

:file

Gzipped VCF file containing variants

*.{vcf.gz}

vcf_indels_tbi{:bash}

meta{:bash}

:map

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

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

:file

Index for gzipped VCF file containing variants

*.{vcf.gz.tbi}

vcf_snvs{:bash}

meta{:bash}

:map

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

*.somatic_snvs.vcf.gz{:bash}

:file

Gzipped VCF file containing variants

*.{vcf.gz}

vcf_snvs_tbi{:bash}

meta{:bash}

:map

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

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

:file

Index for gzipped VCF file containing variants

*.{vcf.gz.tbi}

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

included in
rnadnavarsarek
maintainer
Github user drpatelh
get in touch
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