callHomozygous {RareVariantVis} | R Documentation |
Function calls homozygous regions from whole genome sequencing data.
callHomozygous(sample, chromosomes, caller = "speedseq", MA_Window = 1000, HMZ_length = 100000, min_n_HMZ = 20)
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. |
comp1 |
function calls homozygous regions from whole genome sequencing data and returns them in a tab separated txt file. |
Tomasz Stokowy
# sample = system.file("extdata", "CoriellIndex_S1_chr19_9-10_S1.vcf.recode.vcf.gz", # package = "RareVariantVis") # callHomozygous(sample=sample, chromosomes=c("19"))