callHomozygous: Call homozygous regions from sequencing data

In tstokowy/RareVariantVis: A suite for analysis of rare genomic variants in whole genome 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"))

tstokowy/RareVariantVis documentation built on May 17, 2019, 8:46 p.m.