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 dbdir
- directory with reference databases; this is needed if the
annotcomparfile is not annotated (e.g. a vcf file)
- -callers callers
- callers lists the prefixes for the variant callers to be
used, e.g. 'gatk-rdsbwa- sam-rdsbwa-'. If empty (default) two
callers will be selected from the ones present in the file (in
order of preference: gatkh-rdsbwa- strelka-rdsbwa- gatk-rdsbwa-
sam-rdsbwa-)
- -variantsonly 0/1
- only include positions wich are variant in the sample (so
reference positions are discarded) (default 1)
- -snpsonly 0/1
- only use variants of type snp (default 0)
- -filterrepeats 0/1
- filter out variants in microsatelites or (other) simple
repeats (default 1)
- -quality min
- filter out variants with a quality <= the given value
(default 50)
- -genoqual min
- filter out variants with a genoqual <= the given value
(default 40)
- -htz number
- number of heterozygous snps allowed per window (default 1)
- -density number
- plink --homozyg-density option (default 200)
- -gap number
- plink --homozyg-gap option (default 4000)
- -window number
- 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