Description

TNscope algorithm performs somatic variant calling on the tumor-normal matched pair or the tumor only data, using a Haplotyper algorithm.

Input

name:type
description
pattern

meta{:bash}

:map

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

input{:bash}

:file

One or more BAM or CRAM files.

*.{bam,cram}

input_index{:bash}

:file

Indices for the input files

*.{bai,crai}

intervals{:bash}

:file

bed or interval_list file containing interval in the reference that will be used in the analysis. Only recommended for large WGS data, else the overhead may not be worth the additional parallelisation.

*.{bed,interval_list}

meta2{:bash}

:map

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

fasta{:bash}

:file

Genome fasta file

*.{fa,fasta}

meta3{:bash}

:map

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

fai{:bash}

:file

Index of the genome fasta file

*.fai

meta4{:bash}

:map

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

dbsnp{:bash}

:file

Single Nucleotide Polymorphism database (dbSNP) file

*.vcf.gz

meta5{:bash}

:map

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

dbsnp_tbi{:bash}

:file

Index of the Single Nucleotide Polymorphism database (dbSNP) file

*.vcf.gz.tbi

meta6{:bash}

:map

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

pon{:bash}

:file

Single Nucleotide Polymorphism database (dbSNP) file

*.vcf.gz

meta7{:bash}

:map

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

pon_tbi{:bash}

:file

Index of the Single Nucleotide Polymorphism database (dbSNP) file

*.vcf.gz.tbi

meta8{:bash}

:map

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

cosmic{:bash}

:file

Catalogue of Somatic Mutations in Cancer (COSMIC) VCF file.

*.vcf.gz

meta9{:bash}

:map

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

cosmic_tbi{:bash}

:file

Index of the Catalogue of Somatic Mutations in Cancer (COSMIC) VCF file.

*.vcf.gz.tbi

Output

name:type
description
pattern

vcf{:bash}

meta{:bash}

:map

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

*.vcf.gz{:bash}

:file

VCF file

*.{vcf.gz}

index{:bash}

meta{:bash}

:map

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

*.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
included in
sarek
maintainer
Github user ramprasadn
get in touch
Ask a question on Slack Open an issue on GitHub