modules/sentieon_dnamodelapply

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

dnamodelapplyvcffiltersentieon

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

Description

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

Input

name:type

description

pattern

`meta:map`

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

`vcf:file`

INPUT VCF file

*.{vcf,vcf.gz}

`idx:file`

Index of the input VCF file

*.{tbi}

`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' ]

`ml_model:file`

machine learning model file

*.model

Output

name:type

description

pattern

`vcf`

`meta:map`

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

`*.vcf.gz:file`

INPUT VCF file

*.{vcf,vcf.gz}

`index`

`meta:map`

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

`*.vcf.gz.tbi:file`

Index of the input VCF file

*.{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