callGtFromAd | R Documentation |
call genotype from Allele depth by Frequency
callGtFromAd(x, min.depth = 10, max.depth = 200, low = 0.2, high = 0.8)
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 |
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.
binmapr object, containing genotype slot
Zhougeng Xu
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)
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