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chrchang / plink-ng

A comprehensive update to the PLINK association analysis toolset. Beta testing of the first new version (1.90), focused on speed and memory efficiency improvements, is finishing up. Development is now focused on building out support for multiallelic, phased, and dosage data in PLINK 2.0.
https://www.cog-genomics.org/plink/2.0/
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CNV-SNP LD #244

Closed Qijie0615 closed 1 year ago

Qijie0615 commented 1 year ago

Dear sir or madam. We want to use WGS data to study CNV-SNP LD. How to use PLINK for linkage disequilibrium analysis？ Because the END information seems to be lost after the vcf file of CNV is converted into plink format. This bothers me.

chrchang commented 1 year ago
  1. When you want to keep the VCF END= annotations, you must use plink 2.0 —make-pgen; plink 1.x does not support that.
  2. However, for LD analysis, plink 1.9’s —r2 flag should still be useful.
chrchang commented 1 year ago

(Also, this type of usage question should be asked in the plink2-users Google group, not here.)