I sampled some Pf strains and got them WGS done. Now I want to merge them with existing Pf6 data.
For this I downloaded Pf6 data for all 14 chromosomes. I then used bcftools -view command for filtering out Bangladesh (BD) and Myanmar (MN) samples for each chromosome.
I then used bcftools -merge command to merge BD MN each chromosome vcf file to one big file.
So now I have data for my BD and MN samples for all 14 chromosomes for in a big vcf file. I ran a pca on this using plink ( to convert to bed files and plotted in R). It looked fine,
Now I want to merge my sample WGS vcf file (joint genotypes with combinevcf and genotypevcf command) with the previous big Bangladesh Myanmar pf6 vcf file. I used same way of bzgip tabix and bcftools merge and plink for pca.
But the pca looks absolutely weird. I believe merging my samples with my big pf6 vcf was faulty.
Any help to merge my dataset? Also plink was giving weird errors of duplicate values but I used plink2 and it was party solved.
I’d appreciate any help or advice! Thanks in advance.
I would say that in such cases select a subset of your data, for example, a short ranges of a specific region with SNPS and process the variants off that that subset alone, then visually verify and inspect that the merging process looks the way it should.
Getting "weird errors" with plink seems to indicate something is not quite right with your data.