modules/sentieon_gvcftyper

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

joint genotypinggenotypegvcf

https://github.com/nf-core/modules/[...]/modules/nf-core/sentieon/gvcftyper

Description

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

Input

name:type

description

pattern

`meta:map`

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

]

`gvcfs:file`

gVCF(.gz) file

*.{vcf,vcf.gz}

`tbis:file`

index of gvcf file

*.tbi

`intervals:file`

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

`meta1:map`

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

]

`fasta:file`

Reference fasta file

*.fasta

`meta2:map`

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

]

`fai:file`

Reference fasta index file

*.fai

`meta3:map`

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

]

`dbsnp:file`

dbSNP VCF file

*.vcf.gz

`meta4:map`

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

]

`dbsnp_tbi:file`

dbSNP VCF index file

*.tbi

Output

name:type

description

pattern

`vcf_gz`

`meta:map`

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

]

`*.vcf.gz:file`

VCF file

*.vcf.gz

`vcf_gz_tbi`

`meta:map`

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

]

`*.vcf.gz.tbi:file`

VCF index file

*.vcf.gz.tbi

`versions`

`versions.yml: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