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

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

hapmap plink gwas qc

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written 2.0 years ago by Yugan Gogul Muthukumar •

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

• 0 views • link

written 2.0 years ago by DBScan •

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.

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written 2.0 years ago by Yugan Gogul Muthukumar •

0 answers

No answers yet.