Description

Runs Sentieon’s haplotyper for germline variant calling.

Input

name:type
description
pattern

meta{:bash}

:map

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

input{:bash}

:file

BAM/CRAM file from alignment

*.{bam,cram}

input_index{:bash}

:file

BAI/CRAI file from alignment

*.{bai,crai}

intervals{:bash}

:file

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

recal_table{:bash}

:file

Recalibration table from sentieon/qualcal (optional)

meta2{:bash}

:map

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

fasta{:bash}

:file

Genome fasta file

*.{fa,fasta}

meta3{:bash}

:map

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

fai{:bash}

:file

The index of the FASTA reference.

*.fai

meta4{:bash}

:map

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

dbsnp{:bash}

:file

VCF file containing known sites (optional)

meta5{:bash}

:map

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

dbsnp_tbi{:bash}

:file

VCF index of dbsnp (optional)

emit_vcf{:bash}

: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{:bash}

:boolean

If true, the haplotyper will output a gvcf

Output

name:type
description
pattern

vcf{:bash}

meta{:bash}

:map

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

*.unfiltered.vcf.gz{:bash}

:file

Compressed VCF file

*.unfiltered.vcf.gz

vcf_tbi{:bash}

meta{:bash}

:map

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

*.unfiltered.vcf.gz.tbi{:bash}

:file

Index of VCF file

*.unfiltered.vcf.gz.tbi

gvcf{:bash}

meta{:bash}

:map

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

*.g.vcf.gz{:bash}

:file

Compressed GVCF file

*.g.vcf.gz

gvcf_tbi{:bash}

meta{:bash}

:map

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

*.g.vcf.gz.tbi{:bash}

:file

Index of GVCF file

*.g.vcf.gz.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
sarek
maintainer
Github user asp8200
get in touch
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