modules/sentieon_tnfilter

Filters the raw output of sentieon/tnhaplotyper2.

tnfilterfiltersentieontnhaplotyper2vcf

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

Description

Filters the raw output of sentieon/tnhaplotyper2.

Input

name:type

description

pattern

`meta:map`

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

`vcf:file`

compressed vcf file from tnhaplotyper2

*.vcf.gz

`vcf_tbi:file`

Tabix index of vcf file

*vcf.gz.tbi

`stats:file`

Stats file that pairs with output vcf file

*vcf.gz.stats

`contamination:file`

the location and file name of the file containing the contamination information produced by ContaminationModel.

*.contamination_data.tsv

`segments:file`

the location and file name of the file containing the tumor segments information produced by ContaminationModel.

*.segments

`orientation_priors:file`

the location and file name of the file containing the orientation bias information produced by OrientationBias.

*.orientation_data.tsv

`meta2:map`

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

`fasta:file`

The reference fasta file

*.fasta

`meta3:map`

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

`fai:file`

Index of reference fasta file

*.fasta.fai

Output

name:type

description

pattern

`vcf`

`meta:file`

file containing filtered tnhaplotyper2 calls.

*.vcf.gz

`*.vcf.gz:file`

file containing filtered tnhaplotyper2 calls.

*.vcf.gz

`tbi`

`meta:file`

file containing filtered tnhaplotyper2 calls.

*.vcf.gz

`*.vcf.gz.tbi:file`

tbi file that pairs with vcf.

*.vcf.gz.tbi

`stats`

`meta:file`

file containing filtered tnhaplotyper2 calls.

*.vcf.gz

`*.vcf.gz.stats:file`

file containing statistics of the tnfilter run.

*.stats

`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_tnfilter

Description

Input

`meta:map`

`vcf:file`

`vcf_tbi:file`

`stats:file`

`contamination:file`

`segments:file`

`orientation_priors:file`

`meta2:map`

`fasta:file`

`meta3:map`

`fai:file`

Output

`vcf`

`meta:file`

`*.vcf.gz:file`

`tbi`

`meta:file`

`*.vcf.gz.tbi:file`

`stats`

`meta:file`

`*.vcf.gz.stats:file`

`versions`

`versions.yml:file`

Tools

sentieon

maintainer

get in touch