IBS/IBD, --rel-cutoff and LD pruning -- order of operations

[Maíra R. Rodrigues]

Hi all, 

I'm wondering why the IBS/IBD calculations are recommended to come after LD pruning (https://www.cog-genomics.org/plink/1.9/ibd), while the --rel-cutoff for relationship-based pruning comes before LD pruning in the Order of Operations? (https://www.cog-genomics.org/plink/1.9/order)

Isn't the relationship matrix used in --rel-cutoff based on IBS/IBD calculations? 

Thank you in advance!

Maira 

[Christopher Chang]

1. For historical reasons, LD pruning does not modify the *current* active variant set; it only writes lists of variant IDs to .prune.in and .prune.out files, which must be provided as input to --extract/--exclude later.  So its position in the order of operations, relative to --rel-cutoff and similar operations, is irrelevant.

2. The relationship matrix calculation is entirely separate from the IBS matrix calculation, since it requires variance-standardization that cannot just be applied after the fact on the IBS matrix.