The result of plink --freq is filled with NA
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0
Entering edit mode
6 weeks ago

I downloaded the vcf file. Then I used plink to convert it to a bed file and calculated the array frequency.

However, the result of plink --freq was filled with NA.

Can anyone give us an opinion?

command

① ./plink --vcf ebi-a-GCST010775.vcf.gz --keep-allele-order --out covid --maf 0.2 --make-bed

② wc covid.*

0 1 9194292 covid.bed

9194289 55165734 262203653 covid.bim

1 6 43 covid.fam

30 146 1068 covid.log

③  ./plink --bfile covid --out COVID_1 --freq

④ head -n 5 COVID_1.frq

CHR SNP A1 A2 MAF NCHROBS 1 rs61769339 A G NA 0

1 rs12238997 G A NA 0

1 rs61769351 C G NA 0

1 rs144155419 A G NA 0

1 rs12565286 C G NA 0

--freq vcf SNP NP PLINK • 269 views
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0
Entering edit mode
6 weeks ago

I noticed the mistake bymyself. Downloaded vcf file was GWAS summary statistics.

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