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

]

`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’ ]

`bam` (file)

BAM file.

*.bam

`bai` (file)

BAI file

*.bai

`fasta` (file)

Genome fasta file

*.{fa,fasta}

`fai` (file)

Index of the genome fasta file

*.fai

`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

`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

`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

`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

`meta` (map)

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

]

`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.