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`

`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.