Description

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

Input

name:type
description
pattern

meta{:bash}

:map

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

input{:bash}

:file

BAM/CRAM file(s) from alignment

*.{bam,cram}

input_index{:bash}

:file

BAI/CRAI file(s) from alignment

*.{bai,crai}

intervals{:bash}

:file

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

meta2{:bash}

:map

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

dict{:bash}

:file

GATK sequence dictionary

*.dict

meta3{:bash}

:map

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

fasta{:bash}

:file

Genome fasta file

*.{fa,fasta}

meta4{:bash}

:map

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

fai{:bash}

:file

Index of the genome fasta file

*.fai

meta5{:bash}

:map

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

germline_resource{:bash}

:file

Population vcf of germline sequencing, containing allele fractions.

*.vcf.gz

meta6{:bash}

:map

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

germline_resource_tbi{:bash}

:file

Index file for the germline resource.

*.vcf.gz.tbi

meta7{:bash}

:map

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

panel_of_normals{:bash}

:file

vcf file to be used as a panel of normals.

*.vcf.gz

meta8{:bash}

:map

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

panel_of_normals_tbi{:bash}

:file

Index for the panel of normals.

*.vcf.gz.tbi

emit_orientation_data{:bash}

:boolean

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

emit_contamination_data{:bash}

:boolean

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

Output

name:type
description
pattern

orientation_data{:bash}

meta{:bash}

:map

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

*.orientation_data.tsv{:bash}

:file

TSV file from Sentieon’s algorithm OrientationBias

*.orientation_data.tsv

contamination_data{:bash}

meta{:bash}

:map

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

*.contamination_data.tsv{:bash}

:file

TSV file from Sentieon’s algorithm ContaminationModel

*.contamination_data.tsv

contamination_segments{:bash}

meta{:bash}

:map

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

*.segments{:bash}

:file

Tumour segments file from Sentieon’s algorithm ContaminationModel

*.segments

stats{:bash}

meta{:bash}

:map

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

*.stats{:bash}

:file

Stats file from Sentieon’s algorithm

*.stats

vcf{:bash}

meta{:bash}

:map

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

*.vcf.gz{:bash}

:file

VCF file

*.{vcf.gz}

index{:bash}

meta{:bash}

:map

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

*.vcf.gz.tbi{:bash}

:file

Index of the VCF file

*.vcf.gz.tbi

versions{:bash}

versions.yml{:bash}

: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
maintainer
Github user asp8200
get in touch
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