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’, single_end

]

`meta2` (map)

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

`meta3` (map)

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

`meta4` (map)

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

`meta5` (map)

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

`meta6` (map)

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

`meta7` (map)

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

`meta8` (map)

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

`input` (file)

BAM/CRAM file from alignment

*.{bam,cram}

`input_index` (file)

BAI/CRAI file from alignment

*.{bai,crai}

`intervals` (file)

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

`dict` (file)

GATK sequence dictionary

*.dict

`fasta` (file)

Genome fasta file

*.{fa,fasta}

`fai` (file)

Index of the genome fasta file

*.fai

`germline_resource` (file)

Population vcf of germline sequencing, containing allele fractions.

*.vcf.gz

`germline_resource_tbi` (file)

Index file for the germline resource.

*.vcf.gz.tbi

`panel_of_normals` (file)

vcf file to be used as a panel of normals.

*.vcf.gz

`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

`meta` (map)

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

]

`orientation_data` (file)

TSV file from Sentieon’s algorithm OrientationBias

*.orientation_data.tsv

`contamination_data` (file)

TSV file from Sentieon’s algorithm ContaminationModel

*.contamination_data.tsv

`contamination_segments` (file)

Tumour segments file from Sentieon’s algorithm ContaminationModel

*.segments

`vcf` (file)

VCF file

*.{vcf.gz}

`index` (file)

Index of the VCF file

*.vcf.gz.tbi

`versions` (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.