Troubleshoot non-called variants
I am calling variants on a polyploid plant sample using GATK 4 HaplotypeCaller.
SNP calling works reasonably well, but I see regions where I can clearly see based on the read alignment that there should be SNPs, but these are not called by GATK4. I have been tweaking many parameters, but I don't seem to be possible to get these SNPs in my output VCF file.
Does anyone have any recommendations how I can troubleshoot these false negative SNPs?
Or maybe which parameters I can tweak to get these SNPs to be called?
Thanks a lot!