Description

Runs Sentieon's haplotyper for germline variant calling.

Input

Name
Description
Pattern

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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
Description
Pattern

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Tools

sentieon Documentation

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.

Authors