What do HAP A1 and HAP A2 mean in plink --freqx output?

Question

[_quantum_girl_]

let's assume: SNP1 = A/C, SNP2 = T/G, SNP3 = A/G, SNP4 = C/T

how do I know what C(HAP A1) C(HAP A2) mean? is HAP A1 = ATAC and HAP A2 = CGGT? This wouldn't make a lot of sense since there is a field for each SNP.

I apologize if this is a "newbie" question. But the documentation is not clear to me. An explanation with an example would be very much appreciated :)

Answer 1

[bk11]

Here is what plink manual states-

Allele frequency --freq [{counts | case-control}] ['gz']

--freqx ['gz'] (alias: --frqx)

By itself, --freq writes a minor allele frequency report to plink.frq. If you add the 'counts' modifier, an allele count report is written to plink.frq.count instead. Alternatively, you can use --freq with --within/--family to write a cluster-stratified frequency report to plink.frq.strat, or use the 'case-control' modifier to write a case/control phenotype-stratified report to plink.frq.cc.

--freqx writes a more informative genotype count report to plink.frqx.

For both flags, gzipped output can be requested with the 'gz' modifier.

Nonfounders are normally excluded from these counts/frequencies; use --nonfounders to change this.

All of these reports (except for --freq + --within/--family) are valid input for --read-freq; --freqx is the most powerful when used in that capacity, since it preserves deviation from Hardy-Weinberg equilibrium.

And please see what information are stored in .frqx file-

CHR Chromosome code
SNP Variant identifier
A1  Allele 1 (usually minor)
A2  Allele 2 (usually major)
C(HOM A1)   A1 homozygote count
C(HET)  Heterozygote count
C(HOM A2)   A2 homozygote count
C(HAP A1)   Haploid A1 count (includes male X chromosome)
C(HAP A2)   Haploid A2 count
C(MISSING)  Missing genotype count