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