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Supplementary Data Reumers, De Rijk et al



Genomecomb moved to github on https://github.com/derijkp/genomecomb with documentation on https://derijkp.github.io/genomecomb. For up to date versions, go there. These pages only remain here for the data on the older scientific application (or if someone really needs a long obsolete version of the software)

homwes

Format

cg homwes ?options? variantfile samples ?resultfile?

Summary

finds regions of homozygosity based on a variant file

Description

This command searches for regions of homozygosity for the samples given based on the variant file variantfile. variantfile should preferably be a tab separated (Genomecomb) file with annotations. A vcf file will also be accepted, but dbdir should be given to annotate it. The homozygous regions are stored in resultfile (if resultfile is not given, the name of the resultfile will be based on the variantfile. A directory with the base name of resultfile and extension work will be created that contains all intermidiate data.

Arguments

variantfile
tab separated or vcf file containing variants from exome sequencing
samples
samples to be analysed. If it is the empty, all samples in the file be used
resultfile
file to which the resulting regions of homozygosity will be written. If more than one sample is analysed, it will be a multiregion file containing the comparison of all samples, with the individual results available in fales named resultfileroot-sample.tsv

Options

-dbdir: directory with reference databases; this is needed if the annotcomparfile is not annotated (e.g. a vcf file) ; -callers: default is 'gatk-rdsbwa- sam-rdsbwa-' ; -variantsonly: only include positions wich are variant in the sample (so reference positions are discarded) (default 0) ; -snpsonly: only use variants of type snp (default 0) ; -filterrepeats: filter out variants in microsatelites or (other) simple repeats (default 1) ; -genoqual: filter out variants with a genoqual <= the given value (default 40) ; -htz: number of heterozygous snps allowed per window (default 1) ; -density: plink --homozyg-density option (default 200) ; -gap: plink --homozyg-gap option (default 4000) ; -window: plink --homozyg-window-snp option (default 20)

reference

The homwes tool is described in the following paper (which you should reference when the tool was used)

Kancheva,D, Atkinson,D, De Rijk,P, Zimon,M, Chamova,T, Mitev,V, Yaramis,A, Maria Fabrizi,G, Topaloglu,H, Tournev,I, Parma, Y, Battaloglu, E, Estrada-Cuzcano, A, Jordanova, A (2015)
Novel mutations in genes causing hereditary spastic paraplegia and Charcot-Marie-Tooth neuropathy identified by an optimized protocol for homozygosity mapping based on whole-exome sequencing.
Genet. Med., 10.1038

Category

Analysis