Description

DNAscope algorithm performs an improved version of Haplotype variant calling.

Input

Name (Type)
Description
Pattern

meta (map)

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

]

bam (file)

BAM file.

*.bam

bai (file)

BAI file

*.bai

intervals (file)

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

*.{bed,interval_list}

meta2 (map)

Groovy Map containing meta information for fasta.

fasta (file)

Genome fasta file

*.{fa,fasta}

meta3 (map)

Groovy Map containing meta information for fasta index.

fai (file)

Index of the genome fasta file

*.fai

meta4 (map)

Groovy Map containing meta information for dbsnp.

dbsnp (file)

Single Nucleotide Polymorphism database (dbSNP) file

*.vcf.gz

meta5 (map)

Groovy Map containing meta information for dbsnp_tbi.

dbsnp_tbi (file)

Index of the Single Nucleotide Polymorphism database (dbSNP) file

*.vcf.gz.tbi

meta6 (map)

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

ml_model (file)

machine learning model file

*.model

ml_model (file)

machine learning model file

*.model

pcr_indel_model (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 (string)

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

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
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