How to fix this error while performing QC in PLINK "Warning: 228 het. haploid genotypes present"

Question

[Yugan Gogul Muthukumar]

I was trying to practicing how to perform quality control on Hapmap phase2 data from PLINK site from this link : Link to plink file from Hapmap

I tried using this code

!plink --bfile C:/Users/User/GWAS/HapMap/Data/CEU/Fixed/CEU_fixed --geno 0.05 --maf 0.05 --hwe 1e-6 --make-bed --out C:/Users/User/GWAS/HapMap/Data/CEU/Fixed/QC/your_data_qc1

and when using that on the data, I encountered this error

> Warning: 228 het. haploid genotypes present (see
C:/Users/User/GWAS/HapMap/Data/CEU/Fixed/QC/your_data_qc1.hh ); many commands
treat these as missing.
Warning: Nonmissing nonmale Y chromosome genotype(s) present; many commands
treat these as missing.
Warning: --hwe observation counts vary by more than 10%, due to the X
chromosome.  You may want to use a less stringent --hwe p-value threshold for X
chromosome variants.

Any help is appreciated and I'm still a beginner and never performed GWAS before, you help would be highly appreciated. Thank you in advance and if possible can you also explain the error and why it occurs

[DBScan]

What's the error message? You only show us warnings.

[Yugan Gogul Muthukumar]

sorry I made mistake, here is the entire warning

    PLINK v1.90b7.3 64-bit (4 Aug 2024)            www.cog-genomics.org/plink/1.9/

(C) 2005-2024 Shaun Purcell, Christopher Chang   GNU General Public License v3

Logging to C:/Users/User/GWAS/HapMap/Data/CEU/QC_1/QC_11.log.

Options in effect:

  --bfile C:/Users/User/GWAS/HapMap/Data/CEU/Data_prep/Data_prep_1

  --geno 0.05

  --hwe 1e-6

  --maf 0.05

  --make-bed

  --mind 0.02

  --out C:/Users/User/GWAS/HapMap/Data/CEU/QC_1/QC_11



65315 MB RAM detected; reserving 32657 MB for main workspace.

3967651 variants loaded from .bim file.

90 people (44 males, 46 females) loaded from .fam.

15 people removed due to missing genotype data (--mind).

IDs written to C:/Users/User/GWAS/HapMap/Data/CEU/QC_1/QC_11.irem .

Using 1 thread (no multithreaded calculations invoked).

Before main variant filters, 49 founders and 26 nonfounders present.

Calculating allele frequencies... 10111213141516171819202122232425262728293031323334353637383940414243444546474849505152535455565758596061626364656667686970717273747576777879808182838485868788899091929394959697989 done.

Total genotyping rate in remaining samples is 0.984496.

427810 variants removed due to missing genotype data (--geno).

--hwe: 0 variants removed due to Hardy-Weinberg exact test.

1507581 variants removed due to minor allele threshold(s)

(--maf/--max-maf/--mac/--max-mac).

2032260 variants and 75 people pass filters and QC.

Note: No phenotypes present.

--make-bed to C:/Users/User/GWAS/HapMap/Data/CEU/QC_1/QC_11.bed +

C:/Users/User/GWAS/HapMap/Data/CEU/QC_1/QC_11.bim +

C:/Users/User/GWAS/HapMap/Data/CEU/QC_1/QC_11.fam ... 101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899done.



Warning: 199 het. haploid genotypes present (see

C:/Users/User/GWAS/HapMap/Data/CEU/QC_1/QC_11.hh ); many commands treat these

as missing.

Warning: Nonmissing nonmale Y chromosome genotype(s) present; many commands

treat these as missing.

Warning: --hwe observation counts vary by more than 10%, due to the X

chromosome.  You may want to use a less stringent --hwe p-value threshold for X

chromosome variants.

I just want help with how to resolve this warnings, thank you for responding.