I filtered five VCF files by using GATK tools with option "Select Variants from VCF File" and combine them by "Combine Variants". Now I am interested to check the changes in locus that caused by SNPs and InDels. Which tool I have to used for it?
I am working on rice genotyping, I manually copy and paste the positionof Chromosome in IGV to check that which SNP is present in coding and non coding region but it is tedious and time consuming. Please help me.