Description

Program to compute switch error rate and genotyping error rate given simulated or trio data.

Input

name:type
description
pattern

meta:map

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

estimate:file

Imputed data.

*.{vcf,bcf,vcf.gz,bcf.gz}

estimate_index:file

Index file of the freq VCF/BCF file.

*.{vcf,bcf,vcf.gz,bcf.gz}

region:string

Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000).

chrXX:leftBufferPosition-rightBufferPosition

pedigree:file

Pedigree information in the following format: offspring father mother.

*.{txt, tsv}

meta2:map

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

truth:file

Validation dataset called at the same positions as the imputed file.

*.{vcf,bcf,vcf.gz,bcf.gz}

truth_index:file

Index file of the truth VCF/BCF file.

*.{vcf,bcf,vcf.gz,bcf.gz}

meta3:map

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

freq:file

File containing allele frequencies at each site.

*.{vcf,bcf,vcf.gz,bcf.gz}

freq_index:file

Index file of the freq VCF/BCF file.

*.{vcf.gz.csi,bcf.gz.csi}

Output

name:type
description
pattern

errors

meta:map

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

*.txt.gz:file

Estimates errors from the phased file.

*.txt.gz

versions

versions.yml:file

File containing software versions

versions.yml

Tools

Github user LouisLeNezet
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