I am new to Linux and programming and am trying to use vcftools. I have 3 vcf files; each one is a different population (i.e. with no shared individuals between the files). I am trying to use vcf-isec to merge the 3 files and end up with one vcf file that contains only the SNPs that are present in all 3 files. I have tried the following code:
vcf-isec -n =3 file1.vcf.gz file2.vcf.gz file3.vcf.gz -f -c > CombinedPops.vcf
vcf-isec -n =3 file1.vcf.gz file2.vcf.gz file3.vcf.gz -f > CombinedPops.vcf
but I keep ending up with one file with only the individuals from the first input file. It also gives me a warning that "the number of sample columns is different", but I read in another post that
-f forces vcf-isec to output the file regardless. Could this warning be why I can't get a file with ALL the individuals listed? Can vcf-isec even do this?
Although I have read the vcf-isec documentation, I am still not sure exactly what the difference between the
-o commands are, which may be part of my problem.
Any help is greatly appreciated!