callHomozygous {RareVariantVis} | R Documentation

## Call homozygous regions from sequencing data

### Description

Function calls homozygous regions from whole genome sequencing data.

### Usage

    callHomozygous(sample, chromosomes, caller = "speedseq", MA_Window = 1000, HMZ_length  = 100000, min_n_HMZ = 20)

### Arguments

`sample` | A name of SNV sample file to be analyzed.
`chromosomes` | A vector of strings indicating chromosomes to be analyzed.
`caller` | A string indicating vcf caller. Default is "speedseq", supports "GATK"
`MA_Window` | A number indicating window size for moving average function. Recommended value for genome is 2000, for exome is 20. Default is 1000.
`HMZ_length` | Minimal length of homozygous region to be called. Default is 100000.
`min_n_HMZ` | Minimal number of variants necessary to call a region. Default is 20.

### Value

`comp1` | function calls homozygous regions from whole genome sequencing data and returns them in a tab separated txt file.

### Author(s)

Tomasz Stokowy

### Examples

    # sample = system.file("extdata", "CoriellIndex_S1_chr19_9-10_S1.vcf.recode.vcf.gz",
    #                      package = "RareVariantVis")
    # callHomozygous(sample=sample, chromosomes=c("19"))

[Package RareVariantVis version 2.12.0 Index]