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