modules/sentieon_dnascope

DNAscope algorithm performs an improved version of Haplotype variant calling.

dnascopesentieonvariant_calling

https://github.com/nf-core/modules/[...]/modules/nf-core/sentieon/dnascope

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:false ]

`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

`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

`vcf`

`meta:map`

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

`*.unfiltered.vcf.gz:file`

Compressed VCF file

*.unfiltered.vcf.gz

`vcf_tbi`

`meta:map`

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

`*.unfiltered.vcf.gz.tbi:file`

Index of VCF file

*.unfiltered.vcf.gz.tbi

`gvcf`

`meta:map`

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

`*.g.vcf.gz:file`

Compressed GVCF file

*.g.vcf.gz

`gvcf_tbi`

`meta:map`

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

`*.g.vcf.gz.tbi:file`

Index of GVCF file

*.g.vcf.gz.tbi

`versions`

`versions.yml: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

modules/sentieon_dnascope

Description

Input

`meta:map`

`bam:file`

`bai:file`

`intervals:file`

`meta2:map`

`fasta:file`

`meta3:map`

`fai:file`

`meta4:map`

`dbsnp:file`

`meta5:map`

`dbsnp_tbi:file`

`meta6:map`

`ml_model:file`

`pcr_indel_model:string`

`emit_vcf:string`

`emit_gvcf:boolean`

Output

`vcf`

`meta:map`

`*.unfiltered.vcf.gz:file`

`vcf_tbi`

`meta:map`

`*.unfiltered.vcf.gz.tbi:file`

`gvcf`

`meta:map`

`*.g.vcf.gz:file`

`gvcf_tbi`

`meta:map`

`*.g.vcf.gz.tbi:file`

`versions`

`versions.yml:file`

Tools

sentieon

included in

maintainer

get in touch