How to use GCTA to analyze PCA

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GCTA Analysis of PCA

# method 2:#GCTA analysis PCA # # vcf to bed format plink-- vcf clean.sorted.vcf.gz-- make-bed\-- out all.LDfilter-- allow-extra-chr-- set-missing-var-ids @: #\-- keep-allele-order-- vcf-half-call missing## generates grm text gcta64-- bfile all.LDfilter-autosome-- make-grm-- out GA## for PCA analysis The requirement to be a human being is the digital chromosome: # help document https://cnsgenomics.com/software/gcta/#Datamanagementgcta64-grm GA-pca 20-out PCA_out-threads 10\-maf 0.05

GCTA mainly analyzes human data. If you analyze other animals and plants, you need to renumber the chromatids, otherwise you will report an error:

-- bfile all.LDfilter-autosome--make-grm--out GANote: GRM is computed using the SNPs on the autosome.Reading PLINK FAM file from [all.LDfilter.fam]... 176 individuals to be included from FAM file.176 individuals to be included. 0 males, 0 females, 176 unknown.Reading PLINK BIM file from [all.LDfilter.bim]... Error: Line 36188 of [all.LDfilter.bim] contains illegal chr number, please checkAn error occurs, please check the options or data read here, this article "how to analyze PCA with GCTA" has been introduced. If you want to master the knowledge points of this article, you still need to practice and use it before you can understand it. If you want to know more about related articles, Welcome to the industry information channel.