Linkage_pruning in BCFtools+prune:phased or unphased VCF input file?

Question

[Phismil]

Dear Colleagues, I am wondering if the LD pruning method applied in bcftools+prune plugin required the input VCF file to be phased or alternatively unphased VCF files still can be used?

Many thanks in advance

-l, --max-LD R2 remove sites with r2 bigger than R2 within the -w window

Answer 1

[Phismil]

In case you have the same question, please refer to the answer at: https://github.com/samtools/bcftools/issues/1237 Briefly, unphased data are suitable.