I am working on Rice to call variants using GATK3.3. I have used BWA (bwa mem -M options) to map reads to reference genome. Followed by variant calling (HaplotypeCaller) by following Best Practices of GATK3.3. I have compared the results of 20 genotypes and in all genotypes INDELs are more (2x) as compared to SNPs. Please suggest me on this
Thanks
Mahesh HB