Is it possible to produce this kind of PCA:
https://rstudio-pubs-static.s3.amazonaws.com/89838_c06c544a19f94599aa856576e7c08e2b.html
without EIGENSOFT ? (for some reasons I can't install it in my computer).
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GAPIT can do this for you, too, but it needs other input data: http://www.maizegenetics.net/#!gapit/cmkv For the conversion of VCF to HapMap format, have a look here: Convert Plink Ped Format Into Hapmap Format?
You can also use FlashPCA, esp. because that one shows how to do LD-pruning of SNPs. You can then use the output pcs.txt in the R-script from your link,
SNPs in LD are not independent observations and result in spurious inflation of the distance in PCA.
oh i didn't realize that. i thought the whole point of PCA was to transform correlated, non-independent variables into a finite number of dimensions using a covariance matrix. I didn't realize it mattered if two SNPs were correlated because they were close to each other on the chromosome vs correlated because they both conferred some advantage in a certain environment.
Illumina has a C++ package that does partial PCA on a population VCF directly: https://github.com/Illumina/akt
(In the interest of full disclosure, I work at Illumina, but do not work on this tool)
I recently developed a brand new pca analysis software MingPCACluster that can go from vcf to pca and graph( (VCF2PCA and figture)). Very fast and low memory, accurate and very precise
https://github.com/hewm2008/MingPCACluster
### run without pop.info
# ./bin/MingPCACluster -InVCF Khuman.vcf.gz -OutPut OUT
### run with pop.info
./bin/MingPCACluster -InVCF Khuman.vcf.gz -OutPut OUT -InSampleGroup pop.info
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How about using PLINK to generate the matrix of the VCF files and then do PCA for it.
PLINK has a lot of tools. Which one are you referring to? Is it
pseq proj v-matrix ...?I am not sure actually. But I saw once that with PLINK a SNPs matrix(numerical) were generated. Through this, a PCA would be easy.
Does it perform LD pruning ?
Not sure. You might need to check them out by yourself because I haven't tried it. But I would recommend you to go with @Philipp and @Michs' answers.