Hi!
I got my .vcf files after doing the variant calling with GATK Haplotype caller.
I am new to PLINK, I would like to know how to get a set of PLINK files (.ped, .map) from the vcf file for somatic cells. So far I used the following:
plink --vcf file.vcf --recode --out PLINKfile
But then in the .ped file I have information only about one of the alleles:
person1 person1 0 0 0 -9 G A G C C C ...
person2 person2 0 0 0 -9 G A G C T C ...
person3 person3 0 0 0 -9 G T C C C C ...
As I understand, for SNPs it should have 2 letters at each position, one for each allele, so it should look like this:
person1 person1 0 0 0 -9 GA AA GG CT CC CC ...
person2 person2 0 0 0 -9 GA AA GG CC TC CC ...
person3 person3 0 0 0 -9 GA TA CG CT CC CC ...
How do I do that? Also, is there a way to encode deletions and insertions, especially if they are longer than 1 nucleotide?
Thank you
PLINK has had better support for VCF than .ped files for the last 7 years. I could answer this question, but I would probably be doing you a disservice; you probably shouldn't bother to learn how this format works at all.
The PLINK formats that are actually worth learning about are .bed and .pgen; those are much more efficient than VCF for their purposes.
Thank you!
Actually, I think I found the answer myself: there is a space between two alleles, so actually the first way also includes the information about both alleles, it just prints them in 2 consecutive columns.
My plan was to create .bed, .bim and .fam from .ped and .map afterwards, and run DFAM: family-based association for disease traits. But now I think of it, there probably should be a way to create those files directly from .vcf.
UPD: --make_bed should do it
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ped/map is a very outdated and generally poor and memory inefficient way to store data. Would reccomend using another format if you can.