Friday, September 11, 2015

PLINK2 vs. SNAP for linkage disequilibrium (LD) calculation

Among other ways to calculate SNPs in linkage disequilibrium (LD), two methods have been used in many literatures: PLINK2 and SNAP

With PLINK2, SNPs in LD can be calculated using parameters like:
PLINK2 -r2 dprime --ld-window-kb 1000 --ld-window 10 --ld-window-r2 0.8
SNAP is a web-based service with pre-calculated data: https://www.broadinstitute.org/mpg/snap. You can set the population, distance limit, r2 threshold.

Note that PLINK2 has one more control: --ld-window

In its manual (https://www.cog-genomics.org/plink2/ld), it says "By default, when a limited window report is requested, every pair of variants with at least (10-1) variants between them, or more than 1000 kilobases apart".

That means PLINK2 limits SNPs with two kinds of radius: both the genomic distance (--ld-window-kb) and the number of SNPs apart (--ld-window), while SNAP only has the distance limit. Both of them have the r2 threshold.

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