Allele frequency calculation
Hello everyone,
I use vcf tools to find AF values by using this command:
vcftools --gzvcf $SUBSET_VCF --freq2 --out $OUT --max-alleles 2
The output I got from this is:
chr pos nalleles nchr a1 a2
<dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 22 16050408 2 846 0.944 0.0556
2 22 16050612 2 846 0.937 0.0626
3 22 16050678 2 846 0.948 0.0520
4 22 16050984 2 846 1 0
5 22 16051107 2 846 0.943 0.0567
6 22 16051249 2 846 0.927 0.0733
Now I know in order to find minor allele frequency (MAF): i use this command:
find minor allele frequency
var_freq$maf <- var_freq %>% select(a1, a2) %>% apply(1, function(z) min(z))
But I need to plot total allele frequency and not MAF. Should i consider both a1 and a2 value for plotting?
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