best practice for IBS distance matrix generation

[Matteo Ungaro]

Hi there,

I'm planning on plotting a tree with ggtree using as input a PLINK2.0 IBS distance matrix.

To generate the matrix I'm doing the following:

~/./plink2 --vcf lupine_panel_no-mis.vcf.gz --make-pgen --vcf-half-call m --max-alleles 2 --allow-extra-chr --out lupine_panel_ibs ~/./plink2 --vcf lupine_panel_no-mis.vcf.gz --freq --out lupine_panel_ibs_maf ~/./plink2 --pfile lupine_panel_ibs --make-rel square --read-freq lupine_panel_ibs_maf.afreq --out phylo_tree

​

Then, I've been using the .rel and .rel.id files as input to R, but it appears the format is not compatible... is there anything wrong with what I'm doing, or else should I do something differently?

The .rel file looks like this

1.53578 -0.105267 -0.0945413 -0.083604 -0.209443 -0.139285 -0.208677 -0.199941 -0.209932 -0.130887 -0.082297 -0.0719018 -0.105267 1.60124 -0.142996 -0.023115 -0.243876 -0.0435319 -0.243711 -0.256835 -0.255688 -0.132416 -0.102566 -0.0512363 -0.0945413 -0.142996 1.70865 -0.00168153 -0.229154 -0.0920099 -0.201994 -0.278662 -0.210596 -0.190707 -0.164444 -0.101866 -0.083604 -0.023115 -0.00168153 1.36444 -0.176534 -0.0313074 -0.178905 -0.256911 -0.220043 -0.199516 -0.16628 -0.0265423 -0.209443 -0.243876 -0.229154 -0.176534 1.66881 -0.223521 0.672806 -0.346079 -0.25505 -0.243328 -0.219959 -0.194674 -0.139285 -0.0435319 -0.0920099 -0.0313074 -0.223521 1.6054 -0.209163 -0.304027 -0.216554 -0.225491 -0.186448 0.0659375 -0.208677 -0.243711 -0.201994 -0.178905 0.672806 -0.209163 1.63191 -0.329851 -0.252808 -0.252563 -0.233733 -0.193315 -0.199941 -0.256835 -0.278662 -0.256911 -0.346079 -0.304027 -0.329851 2.72659 -0.253858 -0.0673777 -0.158547 -0.274507 -0.209932 -0.255688 -0.210596 -0.220043 -0.25505 -0.216554 -0.252808 -0.253858 2.45426 -0.233602 -0.159556 -0.186578 -0.130887 -0.132416 -0.190707 -0.199516 -0.243328 -0.225491 -0.252563 -0.0673777 -0.233602 1.91195 -0.0165982 -0.219464 -0.082297 -0.102566 -0.164444 -0.16628 -0.219959 -0.186448 -0.233733 -0.158547 -0.159556 -0.0165982 1.64659 -0.156163 -0.0719018 -0.0512363 -0.101866 -0.0265423 -0.194674 0.0659375 -0.193315 -0.274507 -0.186578 -0.219464 -0.156163 1.41031

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while the .rel.id has this structure

#IID INLUP00165 INLUP00169 INLUP00208 INLUP00214 INLUP00228 INLUP00233 INLUP00245 INLUP00325 INLUP00332 INLUP00393 INLUP00418 INLUP00496

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I looked up a bit, and it seems that ggtree needs a Newick file format. Is this something that I can get from PLINK2.0, or should I attempt to produce it otherwise. In particular, I did the following to organize the matrix-individual information in a single file

grep -v '#' phylo_tree.rel.id | paste -d '\t' - phylo_tree.rel | awk 'BEGIN {print "'$(head -1 phylo_tree.rel.id)'"} {print $0}' | sed 's/\t/ /g' > phylo_tree.phy

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which return the following

#IID INLUP00165 1.53578 -0.105267 -0.0945413 -0.083604 -0.209443 -0.139285 -0.208677 -0.199941 -0.209932 -0.130887 -0.082297 -0.0719018 INLUP00169 -0.105267 1.60124 -0.142996 -0.023115 -0.243876 -0.0435319 -0.243711 -0.256835 -0.255688 -0.132416 -0.102566 -0.0512363 INLUP00208 -0.0945413 -0.142996 1.70865 -0.00168153 -0.229154 -0.0920099 -0.201994 -0.278662 -0.210596 -0.190707 -0.164444 -0.101866 INLUP00214 -0.083604 -0.023115 -0.00168153 1.36444 -0.176534 -0.0313074 -0.178905 -0.256911 -0.220043 -0.199516 -0.16628 -0.0265423 INLUP00228 -0.209443 -0.243876 -0.229154 -0.176534 1.66881 -0.223521 0.672806 -0.346079 -0.25505 -0.243328 -0.219959 -0.194674 INLUP00233 -0.139285 -0.0435319 -0.0920099 -0.0313074 -0.223521 1.6054 -0.209163 -0.304027 -0.216554 -0.225491 -0.186448 0.0659375 INLUP00245 -0.208677 -0.243711 -0.201994 -0.178905 0.672806 -0.209163 1.63191 -0.329851 -0.252808 -0.252563 -0.233733 -0.193315 INLUP00325 -0.199941 -0.256835 -0.278662 -0.256911 -0.346079 -0.304027 -0.329851 2.72659 -0.253858 -0.0673777 -0.158547 -0.274507 INLUP00332 -0.209932 -0.255688 -0.210596 -0.220043 -0.25505 -0.216554 -0.252808 -0.253858 2.45426 -0.233602 -0.159556 -0.186578 INLUP00393 -0.130887 -0.132416 -0.190707 -0.199516 -0.243328 -0.225491 -0.252563 -0.0673777 -0.233602 1.91195 -0.0165982 -0.219464 INLUP00418 -0.082297 -0.102566 -0.164444 -0.16628 -0.219959 -0.186448 -0.233733 -0.158547 -0.159556 -0.0165982 1.64659 -0.156163 INLUP00496 -0.0719018 -0.0512363 -0.101866 -0.0265423 -0.194674 0.0659375 -0.193315 -0.274507 -0.186578 -0.219464 -0.156163 1.41031

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Still, I'm unable to load the matrix in R... any help is much appreciated. Thanks in advance!

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[Christopher Chang]

plink2 doesn't directly generate phylogenetic trees.  You will need to use another program (or R package) to generate a tree from a distance or relationship matrix.

[Chris Chang]

I should have added that the relationship statistic computed by --make-rel is not IBS; for now, use plink 1.9 --ibs-matrix for that.

On Tue, Feb 25, 2025 at 10:57 AM Christopher Chang <chrch...@gmail.com> wrote:

plink2 doesn't directly generate phylogenetic trees.  You will need to use another program (or R package) to generate a tree from a distance or relationship matrix.

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[Matteo Ungaro]

Hi Chris,

    thanks for following up, and sorry for haven't replied on the main thread in my last mail. I see, this was also part of my question and what I'm getting is that in PLINK2.0 at the moment there is no equivalent function to calculate IBS; I'll switch back to v1.9. Thanks!

P. S. in the meantime I managed to get my code to import, wrangle and plot a tree-based representation of a matrix sorted out in R

[Chris Chang]

Incidentally, this is easy to add to plink 2.0 -- as is, you can get an IBS matrix by postprocessing the output of "--make-king-table cols=+ibs1".  It has just been low-priority since the plink 1.9 implementation has been good enough for the use cases I've seen.

To view this discussion visit https://groups.google.com/d/msgid/plink2-users/c974f717-fb83-4e3d-ab33-c9797e36aa8bn%40googlegroups.com.