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’, single_end

]

`bam:file`

BAM file.

*.bam

`bai:file`

BAI file

*.bai

`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’ ]

`cosmic:file`

Single Nucleotide Polymorphism database (dbSNP) file

*.vcf.gz

`cosmic_tbi:file`

Index of the Single Nucleotide Polymorphism database (dbSNP) file

*.vcf.gz.tbi

`meta5:map`

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

`pon:file`

Single Nucleotide Polymorphism database (dbSNP) file

*.vcf.gz

`pon_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’ ]

`dbsnp:file`

Single Nucleotide Polymorphism database (dbSNP) file

*.vcf.gz

`dbsnp_tbi:file`

Index of the Single Nucleotide Polymorphism database (dbSNP) file

*.vcf.gz.tbi

`meta7:map`

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

`interval:file`

bed or interval_list file containing interval in the reference that will be used in the analysis

*.{bed,interval_list}

Output

name:type

description

pattern

`vcf`

`meta:map`

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

]

`*.vcf.gz:file`

VCF file

*.{vcf.gz}

`index`

`meta:map`

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

]

`*.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

modules/sentieon_tnscope

Description

Input

`meta:map`

`bam:file`

`bai:file`

`meta2:map`

`fasta:file`

`meta3:map`

`fai:file`

`meta4:map`

`cosmic:file`

`cosmic_tbi:file`

`meta5:map`

`pon:file`

`pon_tbi:file`

`meta6:map`

`dbsnp:file`

`dbsnp_tbi:file`

`meta7:map`

`interval:file`

Output

`vcf`

`meta:map`

`*.vcf.gz:file`

`index`

`meta:map`

`*.vcf.gz.tbi:file`

`versions`

`versions.yml:file`

Tools

sentieon

maintainer

get in touch