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

]

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}

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}

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

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

errors (file)

Estimates errors from the phased file.

*.txt.gz
author
Github user LouisLeNezet
get in touch
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Tools

shapeit5
MIT

Fast and accurate method for estimation of haplotypes (phasing)

odelaneau.github.io/shapeit5 odelaneau.github.io/shapeit5/docs/documentation https://github.com/odelaneau/shapeit5 10.1101/2022.10.19.512867