modules/sentieon_tnscope

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

tnscopesentieonvariant_calling

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

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:map`

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

`input:file`

One or more BAM or CRAM files.

*.{bam,cram}

`input_index:file`

Indices for the input files

*.{bai,crai}

`intervals: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:map`

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

`fasta:file`

Genome fasta file

*.{fa,fasta}

`meta3:map`

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

`fai:file`

Index of the genome fasta file

*.fai

`meta4:map`

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

`dbsnp:file`

Single Nucleotide Polymorphism database (dbSNP) file

*.vcf.gz

`meta5:map`

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

`dbsnp_tbi:file`

Index of the Single Nucleotide Polymorphism database (dbSNP) file

*.vcf.gz.tbi

`meta6:map`

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

`pon:file`

Single Nucleotide Polymorphism database (dbSNP) file

*.vcf.gz

`meta7:map`

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

`pon_tbi:file`

Index of the Single Nucleotide Polymorphism database (dbSNP) file

*.vcf.gz.tbi

`meta8:map`

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

`cosmic:file`

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

*.vcf.gz

`meta9:map`

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

`cosmic_tbi:file`

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

*.vcf.gz.tbi

Output

name:type

description

pattern

`vcf`

`meta:map`

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

`*.vcf.gz:file`

VCF file

*.{vcf.gz}

`index`

`meta:map`

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

`*.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.

sentieon.com