Description

Perform joint genotyping on one or more samples pre-called with Sentieon’s Haplotyper.

Input

Name (Type)
Description
Pattern

meta (map)

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

]

gvcfs (file)

gVCF(.gz) file

*.{vcf,vcf.gz}

tbis (file)

index of gvcf file

*.tbi

intervals (file)

Interval file with the genomic regions included in the library (optional)

fasta (file)

Reference fasta file

*.fasta

fai (file)

Reference fasta index file

*.fai

dbsnp (file)

dbSNP VCF file

*.vcf.gz

dbsnp_tbi (file)

dbSNP VCF index file

*.tbi

Output

Name (Type)
Description
Pattern

meta (map)

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

]

vcf (file)

Genotyped VCF file

*.vcf.gz

tbi (file)

Tbi index for VCF file

*.vcf.gz

versions (file)

File containing software versions

versions.yml
included in
sarek
maintainer
Github user asp8200
get in touch
Ask a question on Slack Open an issue on GitHub

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