modules/sentieon_haplotyper

Runs Sentieon’s haplotyper for germline variant calling.

sentieonhaplotypecallerhaplotype

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

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)

`recal_table:file`

Recalibration table from sentieon/qualcal (optional)

`meta1:map`

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

]

`fasta:file`

Genome fasta file

*.{fa,fasta}

`meta2:map`

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

]

`fai:file`

The index of the FASTA reference.

*.fai

`meta3:map`

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

]

`dbsnp:file`

VCF file containing known sites (optional)

`meta4:map`

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

]

`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

`vcf`

`meta:map`

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

]

`*.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

]

`*.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

]

`*.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

]

`*.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_haplotyper

Description

Input

`meta:map`

`input:file`

`input_index:file`

`intervals:file`

`recal_table:file`

`meta1:map`

`fasta:file`

`meta2:map`

`fai:file`

`meta3:map`

`dbsnp:file`

`meta4:map`

`dbsnp_tbi:file`

`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