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:false ]

`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:false ]

`fasta`
`:file`

Reference fasta file

*.fasta

`meta2`
`:map`

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

`fai`
`:file`

Reference fasta index file

*.fai

`meta3`
`:map`

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

`dbsnp`
`:file`

dbSNP VCF file

*.vcf.gz

`meta4`
`:map`

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

`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:false ]

`*.vcf.gz`
`:file`

VCF file

*.vcf.gz

`vcf_gz_tbi`

`meta`
`:map`

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

`*.vcf.gz.tbi`
`:file`

VCF index file

*.vcf.gz.tbi

`versions_sentieon`

`${task.process}`
`:string`

The process the versions were collected from

`sentieon`
`:string`

The tool name

`sentieon driver --version | sed "s/.*-//g"`
`:string`

The command used to generate the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The process the versions were collected from

`sentieon`
`:string`

The tool name

`sentieon driver --version | sed "s/.*-//g"`
`:string`

The command used to generate the version of the tool

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

modules/sentieon_gvcftyper

Description

Input

`meta`
`:map`

`gvcfs`
`:file`

`tbis`
`:file`

`intervals`
`:file`

`meta1`
`:map`

`fasta`
`:file`

`meta2`
`:map`

`fai`
`:file`

`meta3`
`:map`

`dbsnp`
`:file`

`meta4`
`:map`

`dbsnp_tbi`
`:file`

Output

`vcf_gz`

`meta`
`:map`

`*.vcf.gz`
`:file`

`vcf_gz_tbi`

`meta`
`:map`

`*.vcf.gz.tbi`
`:file`

`versions_sentieon`

`${task.process}`
`:string`

`sentieon`
`:string`

`sentieon driver --version | sed "s/.*-//g"`
`:string`

Topics

`versions`

`${task.process}`
`:string`

`sentieon`
`:string`

`sentieon driver --version | sed "s/.*-//g"`
`:string`

Tools

sentieon

included in

maintainer

get in touch

modules/sentieon_gvcftyper

Description

Input

meta:map

gvcfs:file

tbis:file

intervals:file

meta1:map

fasta:file

meta2:map

fai:file

meta3:map

dbsnp:file

meta4:map

dbsnp_tbi:file

Output

vcf_gz

meta:map

*.vcf.gz:file

vcf_gz_tbi

meta:map

*.vcf.gz.tbi:file

versions_sentieon

${task.process}:string

sentieon:string

sentieon driver --version | sed "s/.*-//g":string

Topics

versions

${task.process}:string

sentieon:string

sentieon driver --version | sed "s/.*-//g":string

Tools

sentieon

included in

maintainer

get in touch

`meta`
`:map`

`gvcfs`
`:file`

`tbis`
`:file`

`intervals`
`:file`

`meta1`
`:map`

`fasta`
`:file`

`meta2`
`:map`

`fai`
`:file`

`meta3`
`:map`

`dbsnp`
`:file`

`meta4`
`:map`

`dbsnp_tbi`
`:file`

`vcf_gz`

`meta`
`:map`

`*.vcf.gz`
`:file`

`vcf_gz_tbi`

`meta`
`:map`

`*.vcf.gz.tbi`
`:file`

`versions_sentieon`

`${task.process}`
`:string`

`sentieon`
`:string`

`sentieon driver --version | sed "s/.*-//g"`
`:string`

`versions`

`${task.process}`
`:string`

`sentieon`
`:string`

`sentieon driver --version | sed "s/.*-//g"`
`:string`