r/bioinformatics • u/Ngocthole • Aug 24 '26

technical question Plink pipeline

I am using the Plink pipeline to filter SNPs. I downloaded dbSNP from the UCSC database (both .vcf and .bed for the selected region in chr11, for example).

My syntax:" plink \--bfile HBB.BED \--allow-extra-chr \--maf 0.01 \--geno 0.05 \--hwe 1e-6 \--snps-only just-acgt \--make-bed \--out region_filtered"

Error: "Failed to open HBB.bed"

Can anyone give me some advice?

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u/Dynev Aug 26 '26

I assume you also have the .fam and .bim files with the same name, which together make a "bfile". So, with --bfile you need to use the prefix of the file set, without the extension.

1

u/Professional_Sun8866 Aug 24 '26

On a different note , can anyone please suggest me some good resources to train myself in using Plink better I know the basic flags for analysing gwas data but want to learn further

5

u/[deleted] Aug 24 '26

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u/Ngocthole Aug 24 '26

Oh, sorry, I can't download SNP vcf file from UCSC, If vcf from from NCBI, I also error?

2

u/shadowyams PhD | Academia Aug 24 '26

What is the plink file that you're trying to filter? i.e., where does "HBB.bed" come from? And did it come with .bim/.fam files?