modules/sentieon_tnhaplotyper2

Tnhaplotyper2 performs somatic variant calling on the tumor-normal matched pairs.

tnseqtnhaplotyper2sentieonvariant_calling

https://github.com/nf-core/modules/[...]/modules/nf-core/sentieon/tnhaplotyper2

Description

Tnhaplotyper2 performs somatic variant calling on the tumor-normal matched pairs.

Input

name:type

description

pattern

`meta`
`:map`

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

`input`
`:file`

BAM/CRAM file(s) from alignment

*.{bam,cram}

`input_index`
`:file`

BAI/CRAI file(s) from alignment

*.{bai,crai}

`intervals`
`:file`

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

`meta2`
`:map`

Groovy Map containing reference information. e.g. [ id:‘test’ ]

`dict`
`:file`

GATK sequence dictionary

*.dict

`meta3`
`:map`

Groovy Map containing reference information. e.g. [ id:‘test’ ]

`fasta`
`:file`

Genome fasta file

*.{fa,fasta}

`meta4`
`:map`

Groovy Map containing reference information. e.g. [ id:‘test’ ]

`fai`
`:file`

Index of the genome fasta file

*.fai

`meta5`
`:map`

Groovy Map containing reference information. e.g. [ id:‘test’ ]

`germline_resource`
`:file`

Population vcf of germline sequencing, containing allele fractions.

*.vcf.gz

`meta6`
`:map`

Groovy Map containing reference information. e.g. [ id:‘test’ ]

`germline_resource_tbi`
`:file`

Index file for the germline resource.

*.vcf.gz.tbi

`meta7`
`:map`

Groovy Map containing reference information. e.g. [ id:‘test’ ]

`panel_of_normals`
`:file`

vcf file to be used as a panel of normals.

*.vcf.gz

`meta8`
`:map`

Groovy Map containing reference information. e.g. [ id:‘test’ ]

`panel_of_normals_tbi`
`:file`

Index for the panel of normals.

*.vcf.gz.tbi

`emit_orientation_data`
`:boolean`

If true, the module will run the sentieon algorithm TNhaplotyper2 followed by the sentieon algorithm OrientationBias.

`emit_contamination_data`
`:boolean`

If true, the module will run the sentieon algorithm TNhaplotyper2 followed by the sentieon algorithm ContaminationModel.

Output

name:type

description

pattern

`orientation_data`

`meta`
`:map`

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

`*.orientation_data.tsv`
`:file`

TSV file from Sentieon’s algorithm OrientationBias

*.orientation_data.tsv

`contamination_data`

`meta`
`:map`

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

`*.contamination_data.tsv`
`:file`

TSV file from Sentieon’s algorithm ContaminationModel

*.contamination_data.tsv

`contamination_segments`

`meta`
`:map`

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

`*.segments`
`:file`

Tumour segments file from Sentieon’s algorithm ContaminationModel

*.segments

`stats`

`meta`
`:map`

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

`*.stats`
`:file`

Stats file from Sentieon’s algorithm

*.stats

`vcf`

`meta`
`:map`

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

`*.vcf.gz`
`:file`

VCF file

*.{vcf.gz}

`index`

`meta`
`:map`

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

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

Index of the VCF 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.