callGtFromAd: call genotype from Allele depth by Frequency

In xuzhougeng/binmapr: Call Marker from SNP Data using Binmap

call genotype from Allele depth by Frequency

Description

call genotype from Allele depth by Frequency

Usage

callGtFromAd(x, min.depth = 10, max.depth = 200, low = 0.2, high = 0.8)

Arguments

x	a binmapr object
min.depth	minimum depth to infer the genotype, if depth lower than it, it will be conside as NA
max.depth	maximum depth to infer the genotype, if depth larger than it, it will be conside as NA
low	threshold to infer one parent, encoded as 0
high	threshold to infer another parent, encoded as 2

Details

The original GT in VCF may be wrong, if the variant is sequencing error. To avoid this kind of error, we used the ALT/(REF + ALT) to infer the genotype. If the ratio <= 0.2, it will be encoded as 0. If the ratio >= 0.8, it will be encoded as 2. Otherwise, it will be encoded as 1.

Value

binmapr object, containing genotype slot

Author(s)

Zhougeng Xu

Examples

AD <- matrix(data = c("30,1","1,30","0,0","15,15"), nrow = 2)
row.names(AD) <- c("chr1_1","chr1_100")
colnames(AD) <- c("A","B")
geno <- callGtFromAd(AD)

xuzhougeng/binmapr documentation built on Aug. 25, 2023, 6:44 a.m.