Description

Filters the raw output of sentieon/tnhaplotyper2.

Input

name:type
description
pattern

meta{:bash}

:map

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

vcf{:bash}

:file

compressed vcf file from tnhaplotyper2

*.vcf.gz

vcf_tbi{:bash}

:file

Tabix index of vcf file

*vcf.gz.tbi

stats{:bash}

:file

Stats file that pairs with output vcf file

*vcf.gz.stats

contamination{:bash}

:file

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

*.contamination_data.tsv

segments{:bash}

:file

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

*.segments

orientation_priors{:bash}

:file

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

*.orientation_data.tsv

meta2{:bash}

:map

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

fasta{:bash}

:file

The reference fasta file

*.fasta

meta3{:bash}

:map

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

fai{:bash}

:file

Index of reference fasta file

*.fasta.fai

Output

name:type
description
pattern

vcf{:bash}

meta{:bash}

:file

file containing filtered tnhaplotyper2 calls.

*.vcf.gz

*.vcf.gz{:bash}

:file

file containing filtered tnhaplotyper2 calls.

*.vcf.gz

tbi{:bash}

meta{:bash}

:file

file containing filtered tnhaplotyper2 calls.

*.vcf.gz

*.vcf.gz.tbi{:bash}

:file

tbi file that pairs with vcf.

*.vcf.gz.tbi

stats{:bash}

meta{:bash}

:file

file containing filtered tnhaplotyper2 calls.

*.vcf.gz

*.vcf.gz.stats{:bash}

:file

file containing statistics of the tnfilter run.

*.stats

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
maintainer
Github user asp8200
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