Description

modifies the input VCF file by adding the MLrejected FILTER to the variants

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]

vcf{:bash}

:file

INPUT VCF file

*.{vcf,vcf.gz}

idx{:bash}

:file

Index of the input VCF file

*.{tbi}

meta2{:bash}

:map

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

fasta{:bash}

:file

Genome fasta file

*.{fa,fasta}

meta3{:bash}

:map

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

fai{:bash}

:file

Index of the genome fasta file

*.fai

meta4{:bash}

:map

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

ml_model{:bash}

:file

machine learning model file

*.model

Output

name:type
description
pattern

vcf{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]

*.vcf.gz{:bash}

:file

INPUT VCF file

*.{vcf,vcf.gz}

tbi{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]

*.vcf.gz.tbi{:bash}

:file

Index of the input VCF file

*.{tbi}

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
included in
rarediseasesarek
maintainer
Github user ramprasadn
get in touch
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