plink --indep LD calculation and filtering to VCF file in one command

Question

[rjzotti]

I want to use plink's linkage disequilibrium feature to filter my VCF file. I'm new to genomics, but after reading plink's documentation, I assumed I could do this in one command:

plink \
--bcf /input/${CHROMOSOME_ID}.vcf.gz \
--indep $LD_WINDOW_SIZE_KB $LD_STEP_SIZE $VIF_THRESHOLD \
--recode vcf \
--out /output/ch${CHROMOSOME_ID} \
--allow-extra-chr

I then use the output file, e.g., ch6.vcf, for downstream analysis. I never bothered touching the .in and .out files because according to the plink data docs:

--recode creates a new text fileset, after applying sample/variant filters and other operations.

so I assumed plink's --recode would interpret my $VIF_THRESHOLD as a variant filter operation. However, in other, older biostars posts I've read that you have to do the filtering using .in or .out in a separate command. Is my original command incorrect?

Answer 1

[Sam]

Based on my understanding, --indep doesn't perform filtering, but generate file containing the pruned SNPs. So you should do --extract or --exclude in downstream analysis to filter out the SNPs. Documentation is here