HIBLUP can calculate allele frequency and genotype frequency for markers.

Allele frequency

If the flag --allele-freq is detected in the input command, HIBLUP will calculate A1 allele frequency for all SNPs in genotype:

./hiblup --bfile demo --allele-freq --out demo

It will generate a file named demo.afreq, brief view of this file:

SNP     a1  a2  freq_a1
snp1    A   C   0.2775
snp2    G   T   0.4475
snp3    A   G   0.1918

Then users can filter SNPs with a specific condition, for example, pick up SNPs at the condition of 0.05 < freq <= 0.1:

awk '$4 > 0.05 && $4 <= 0.1 {print $1}' demo.afreq > freq_filter_snp.txt

Genotype frequency

If the flag --geno-freq is detected in the input command, HIBLUP will calculate the genotype frequency of A1A1 and A2A2 for all SNPs in genotype:

./hiblup --bfile demo --geno-freq --out demo

It will generate a file named demo.gfreq, brief view of this file:

SNP     a1  a2  freq_a1a1  freq_a2a2
snp1    A   C    0.3456     0.1244
snp2    G   T    0.2358     0.2345
snp3    A   G    0.1395     0.4643