We are working on some project to check concordance between Genotype Sample and NGS sample. We are using MEGA Genotype Array. We have processed genotype sample using GenomeStudio from Illumina and following procedure given at Is there a tool to transform GenomeStudio genotype format to VCF? .
Generated (Genotype) VCF has some very weird entries with Chromosome as 0 and Position as 0 as well. I am not sure why these entries are coming with Genotype VCF. As we are using same genotype file for concordance with Sequencing VCF file and we are getting concordance around 80-85% only which ideally should be more then 90%. Could some one help me with some additional input about any improvements specially why We are getting Chromosome as 0 and Position as 0 . Apart from this we are not getting QUAL score as well for any of VCF entries .