We have have genotype data (SNPs) on 50 K markers using Illumina SNP array. We now have fully sequenced these animals using NGS paired end sequencing and called SNPs on them using GATK. I was wondering if there was a tool or a way to see the concordance between the SNPs called using both programs since the GATK output is vcf format where as the genotypes using the array are in plink format. I know this could be tricky since some variants in GATK maybe called on the positive strand and some on the negative strand. However, I have looked for a solution online and there seems to be no straight way of doing this.
I would really appreciate any help with this.