Description

DNAscope algorithm performs an improved version of Haplotype variant calling.

Input

name:type
description
pattern

meta{:bash}

:map

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

bam{:bash}

:file

BAM file.

*.bam

bai{:bash}

:file

BAI file

*.bai

intervals{:bash}

:file

bed or interval_list file containing interval in the reference that will be used in the analysis

*.{bed,interval_list}

meta2{:bash}

:map

Groovy Map containing meta information for fasta.

fasta{:bash}

:file

Genome fasta file

*.{fa,fasta}

meta3{:bash}

:map

Groovy Map containing meta information for fasta index.

fai{:bash}

:file

Index of the genome fasta file

*.fai

meta4{:bash}

:map

Groovy Map containing meta information for dbsnp.

dbsnp{:bash}

:file

Single Nucleotide Polymorphism database (dbSNP) file

*.vcf.gz

meta5{:bash}

:map

Groovy Map containing meta information for dbsnp_tbi.

dbsnp_tbi{:bash}

:file

Index of the Single Nucleotide Polymorphism database (dbSNP) file

*.vcf.gz.tbi

meta6{:bash}

:map

Groovy Map containing meta information for machine learning model for Dnascope.

ml_model{:bash}

:file

machine learning model file

*.model

pcr_indel_model{:bash}

:string

Controls the option pcr_indel_model for Dnascope. The possible options are “NONE” (used for PCR free samples), and “HOSTILE”, “AGGRESSIVE” and “CONSERVATIVE”. See Sentieons documentation for further explanation.

emit_vcf{:bash}

:string

Controls the vcf output from Dnascope. Possible options are “all”, “confident” and “variant”. See Sentieons documentation for further explanation.

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
rarediseasesarek
maintainer
Github user ramprasadn
get in touch
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