Description

Perform joint genotyping on one or more samples pre-called with Sentieon’s Haplotyper.

Input

name:type
description
pattern

meta{:bash}

:map

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

gvcfs{:bash}

:file

gVCF(.gz) file

*.{vcf,vcf.gz}

tbis{:bash}

:file

index of gvcf file

*.tbi

intervals{:bash}

:file

Interval file with the genomic regions included in the library (optional)

meta1{:bash}

:map

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

fasta{:bash}

:file

Reference fasta file

*.fasta

meta2{:bash}

:map

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

fai{:bash}

:file

Reference fasta index file

*.fai

meta3{:bash}

:map

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

dbsnp{:bash}

:file

dbSNP VCF file

*.vcf.gz

meta4{:bash}

:map

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

dbsnp_tbi{:bash}

:file

dbSNP VCF index file

*.tbi

Output

name:type
description
pattern

vcf_gz{:bash}

meta{:bash}

:map

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

*.vcf.gz{:bash}

:file

VCF file

*.vcf.gz

vcf_gz_tbi{:bash}

meta{:bash}

:map

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

*.vcf.gz.tbi{:bash}

:file

VCF index file

*.vcf.gz.tbi

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

sentieon

Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.

sentieon.com
included in
sarek
maintainer
Github user asp8200
get in touch
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