Hello friends,
I called SNPs using Freebayes and also used snpeff to see the effects on the output file from Freebayes. The number of SNPs for the same .vcf file is different in these two programs. Is there any suitable explanation for this? Number of SNPs reported by snpeff on the Freebayes output file is higher than the number of SNPs counted in Freebayes.
Thanks for your help