invalid --hwe parameter sequence error when doing QC

Hi, all -

Been running this statement to conduct a QC:

plink --bfile ft_maf --hwe 1e-50 keep-fewhet --make-bed --out ft_hwe_gt

However, that keeps on giving me a "Error: Invalid --hwe parameter sequence."

What is wrong?

• 1,121 views • link

updated 3.5 years ago by chrchang523

• written 3.5 years ago by Karan •

1 answer

The 'keep-fewhet' modifier requires PLINK 2.0; you are using PLINK 1.9 here.

• 0 views • link

written 3.5 years ago by chrchang523

More posts like this

How to fix this error while performing QC in PLINK "Warning: 228 het. haploid genotypes present"
written 2.0 years ago by 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 …
There are several lines in Manhattan plot.
written 2.6 years ago by kgwkk2 •

![enter image description here][1] [1]: /media/images/ca0fe8b9-6719-4878-82ad-0b6ee8f7 I generated Manhattan plot with multi-calling vcf file. But when I got the result, there were several weird lines …
PLINK basic command line usage
written 4.9 years ago by Phylicia •

Hey, I am new to PLINK. I run a tutorial of how to calculate polygenic risk score under a tutorial. https://choishingwan.github.io/PRS-Tutorial/target/#standard-gwas-qc I run the part …
GCTA make GRM error contains illegal chr number
written 5.1 years ago by Star:) •

Hi I created bim, fam, and bed files by Plink with the use of these codes. > shell("plink --file r --maf 0.05 --geno 0.01 --mind …
plink : Batch effect issues after merge of two datasets
written 5.4 years ago by Nicolas Rosewick

Hi, I merged two plink dataset using # take only SNP present in both datasets plink --keep-allele-order --bfile dataset_A --extract snp_in_common.txt --make-bed --out dataset_A_common plink …
Unused command line option: --make-just-fam
written 5.4 years ago by suraj.adewale1 •

We are trying to run the plink command for QC plink \ --bfile EUR \ --maf 0.01 \ --hwe 1e-6 \ --geno 0.01 \ --mind …
Reorder filter options in PLINK
written 5.5 years ago by panacotaforcota •

Dear All, I try to make QC steps in PLINK, but I faced problem with order of steps. For example, I want such order: --bfile …
Plink with hwe option does not work
written 6.2 years ago by east_chenyutang •

Hi all, I am new to Plink, I was trying to extract SNPs based on base position with filters like maf and hwe, below are …
how to do QC on data imputed on Michigan Imputation Server?
written 6.3 years ago by anamaria

Hello, I had .CEL files and than I converted those to plink format and did QC steps following https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6001694/ Then imputed those SNPs on Michigan …
How to remove duplicate SNPs from plink ped,vcf?
written 8.2 years ago by Tania

**Hi Every one** I used to get this error when I try to split a vcf I get from plink format: > [E::bcf_hdr_add_sample] Duplicated sample …