I am trying to generate the phylogenetic tree of 9 sheep breeds based on the snps of their mitochodrial genomes.
The steps that I follow are:
- Calculation of the snps of all the individuals with three different tools: samtools, freebayes, gatk.
- Calculation of the intersection of the snps for each individual.
- Merging them all in one vcf file in order to generate a pedigree file (PED) with all the genotypes (I used vcftools for the merging and PDSpider for the vcf to ped conversion).
- Distant matrix generation with PLINK.
In that point I am getting the following error from PLINK:
ERROR: No nonmissing markers for individuals
Unfortunately I cannot understand this error and obviously I cannot find a way to fix it.
I would appreciate your help with that or some other suggestion about the steps that I follow.
Thank you very much in advance,