Re: Error in PLINK2 filtering

[Chris Chang]

Always post full .log file(s) when asking for troubleshooting help.

On Wed, Sep 17, 2025 at 7:21 AM 陈泓朴 <otis....@gmail.com> wrote:

Hi there, thank you for developing this great tool.

I am using PLINK2 to obtain the PLINK BED file as the input to construct sparse GRM.

However, I encountered the conflict of frequency filtering. The problem is that even though I've already specified `maf` threshold, it turned out that there were still variants with minor allele frequency < 0.01.

Code:

```

threadNum=32
memNum=5000  # in Mb
##
LD_window_size=50
LD_window_step=10
LD_r2=0.1
maf=0.01
mac=1  ## None
geno=0.1
hwe=1e-15

plink2 --bfile ../GWAS.plink.17K/ALL_germline.chr${id}.normed.vcf --keep ${sample_file} --indep-pairwise ${LD_window_size} ${LD_window_step} ${LD_r2} --maf ${maf} --mac ${mac} --geno ${geno} --hwe ${hwe} --threads ${threadNum} --memory ${memNum} --out ${output_path}/${output_prefix}

```

I'll really appreciate it if you could give me a hint.

Hongpu,

Best.

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