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 ]

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' ]

vcf (file)

INPUT VCF file

*.{vcf,vcf.gz}

idx (file)

Index of the input VCF file

*.{tbi}

fasta (file)

Genome fasta file

*.{fa,fasta}

fai (file)

Index of the genome fasta file

*.fai

ml_model (file)

machine learning model file

*.model

Output

Name (Type)
Description
Pattern

meta (map)

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

versions (file)

File containing software versions

versions.yml

vcf (file)

INPUT VCF file

*.{vcf,vcf.gz}

index (file)

Index of the input VCF file

*.{tbi}
included in
raredisease sarek
maintainer
Github user ramprasadn
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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