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

HIBLUP can also supports to compute allele frequency for sub-groups, supposing that there are mixed groups in binary genotype file, we are interested in the distribution or comparing the difference of allele frequency among groups, it is easy to implement by specifying a population classification file (see file format here) to the option “--pop-class” when running HIBLUP, for example:

./hiblup --bfile demo --allele-freq --pop-class demo.popclass.txt --out demo

Then the allele frequency of different groups will be listed by columns:

SNP     a1  a2  DD_freq_a1  YY_freq_a1  LL_freq_a1
snp1    A   C   0.2353      0.1245      0.5423
snp2    G   T   0.1235      0.3456      0.2356
snp3    A   G   0.0235      0.1224      0.2123

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

As described above, HIBLUP also supports to compute genotype frequency for sub-groups, just specify a population classification file to option “--pop-class” when running “--geno-freq“.