3. Check sample heterozygosity (Sample-level)

Heterozygosity refers to the presence of each of the two alleles at a given SNP within an individual. Outliers showing excess or depletion in heterozygotes genotypes may be due to contamination or issues during genotyping process.

Note

Consider doing it already only with high call rate SNPs?

runPLINK("--ped file.ped --map file.map --het --out file")
system("cat file.het | tr -s ' ' '\t' > file_het.tabs")
het_level <- read.delim ("file_het.tabs") %>%
  select (-X)

Plot sample call rate vs heterozygosity

sample_missing_rate_het <- call_rate_samples_after_filter %>%
        left_join(het_level, by = c("IID" = "IID")) %>%
        rename(heter_rate = "F")
std = sd(sample_missing_rate_het$heter_rate) ## calculate standard deviation
std_list = c(std, -std, 2*std, -2*std, 3*std, -3*std)

ggplot(sample_missing_rate_het, aes(x= F_MISS, y= heter_rate)) +
        geom_point() +
        geom_vline(xintercept = 0.1, linetype="dashed", color = "blue") +
        geom_hline(yintercept = std_list[1:4], col = "grey", linetype = "dashed") +
        geom_hline(yintercept = std_list[5:6], col = "red", linetype = "dashed") +
        ggtitle("Heterozygosity vs Missingness across samples") +
        theme_bw() +
        xlab("Proportion of missing SNPs") +
        ylab("Heterozygosity rate(+- 3 sd)")

Note

Advice Exclude samples with more than 3 standard deviations away from mean heterozygosity.

Lifelines uses 4sd from the mean heterozygosity.