LD SNP pruning with plink

Question

[celia]

Hi guys! I have a big dataset of SNPs divided into different files based on the chromosomes. I have already performed some filtering analysis, and now, I need to prune the LD SNPs, which I will use for genomic prediction analysis. However, I cannot filter the LD pruned SNPs as Plink does not seem to find any, so the plink.prune.in and .out files are not being produced. Is there something that I am missing? Why is this happening?

My organism is chickpea. Having .hmp.txt files initially, I obtained the .map and .ped files using the Tassel 5 software. The files for the first chromosome are named Ca1_filt.plk.map and Ca1_filt.plk.ped. The command that I used for the SNPs of the chromosome 1 is:

plink --file Ca1_filt.plk --indep-pairwise 50 10 0.2 --out Ca1_out --allow-extra-chr

The output is:

PLINK v1.90b6.21 64-bit (19 Oct 2020)          www.cog-genomics.org/plink/1.9/
(C) 2005-2020 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to Ca1_out.log.
Options in effect:
  --allow-extra-chr
  --file Ca1_filt.plk
  --indep-pairphase 50 10 0.2
  --out Ca1_out

257111 MB RAM detected; reserving 128555 MB for main workspace.
.ped scan complete (for binary autoconversion).
Performing single-pass .bed write (56621 variants, 3171 people).
--file: Ca1_out-temporary.bed + Ca1_out-temporary.bim + Ca1_out-temporary.fam
written.
56621 variants loaded from .bim file.
3171 people (0 males, 0 females, 3171 ambiguous) loaded from .fam.
Ambiguous sex IDs written to Ca1_out.nosex .
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 0 founders and 3171 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.921514.
56621 variants and 3171 people pass filters and QC.
Note: No phenotypes present.
Warning: Skipping --indep-pairphase since there are less than two founders.
(--make-founders may come in handy here.)

Thank you very much for your help.

[Ram]

Please do not use bioinformatics as a tag unless your post is about the field of bioinformatics itself. For proper examples, please see Forum and News type posts under https://www.biostars.org/tag/bioinformatics/

I've removed the tag this time but please be more mindful in the future.

Answer 1

[Nicolas Rosewick]

As mention in the logs :

Warning: Skipping --indep-pairphase since there are less than two founders.

You can try adding --nonfounders as parameter and rerun the plink command

[celia]

Thank you very much. After some trials, I think adding --make-founders worked for me. Do you think that is not a good idea? Adding --nonfounders did not work.

Cheers