Description

Runs Sentieon’s haplotyper for germline variant calling.

Input

Name (Type)
Description
Pattern

meta (map)

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

]

input (file)

BAM/CRAM file from alignment

*.{bam,cram}

input_index (file)

BAI/CRAI file from alignment

*.{bai,crai}

intervals (file)

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

fasta (file)

Genome fasta file

*.{fa,fasta}

fai (file)

The index of the FASTA reference.

*.fai

dbsnp (file)

VCF file containing known sites (optional)

dbsnp_tbi (file)

VCF index of dbsnp (optional)

emit_vcf (string)

Controls the vcf output from the haplotyper.
If emit_vcf is set to “all” then the haplotyper will output a vcf generated by the haplotyper in emit-mode “all”.
If emit_vcf is set to “confident” then the haplotyper will output a vcf generated by the haplotyper in emit-mode “confident”.
If emit_vcf is set to “variant” then the haplotyper will output a vcf generated by the haplotyper in emit_mode “confident”.

emit_gvcf (boolean)

If true, the haplotyper will output a gvcf

Output

Name (Type)
Description
Pattern

meta (map)

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

]

vcf (file)

Compressed VCF file

*.unfiltered.vcf.gz

vcf_tbi (file)

Index of VCF file

*.unfiltered.vcf.gz.tbi

gvcf (file)

Compressed GVCF file

*.g.vcf.gz

gvcf_tbi (file)

Index of GVCF file

*.g.vcf.gz.tbi

versions (file)

File containing software versions

versions.yml
included in
sarek
maintainer
Github user asp8200
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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