Peds5000+Vespa8000 Ininital genotyping

Call Rate for samples

dat <- read.table("peds5000_vespa8000_original_call_Samples_Table.txt", sep = "\t", 
    header = TRUE)
summary(dat$Call.Rate)

##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##   0.000   0.990   0.991   0.980   0.991   0.992

cutoff <- c(0.8, seq(from = 0.9, to = 0.99, by = 0.01))
exclude.samples <- data.frame(cutoff = paste("<", cutoff, sep = ""))
for (i in 1:length(cutoff)) {
    exclude.samples$number[i] <- sum(dat$Call.Rate < cutoff[i])
}
print(exclude.samples)

##    cutoff number
## 1    <0.8    259
## 2    <0.9    363
## 3   <0.91    387
## 4   <0.92    419
## 5   <0.93    446
## 6   <0.94    485
## 7   <0.95    549
## 8   <0.96    661
## 9   <0.97    831
## 10  <0.98   1035
## 11  <0.99   4278

hist(dat$Call.Rate, xlab = "Call Rate", main = "Histogram of sample call rate", 
    breaks = 50)