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2/50 ind show ./. at almost all positions in final vcf even though there is data
I used HaplotypeCaller to generate VCF from 50 individuals. My reference is Rattus norvegicus and 48/50 individuals are Rattus norvegicus. The remaining two individuals are Rattus rattus species. The WGS for these two individuals have been mapped on the same reference, Rattus norvegicus, as the other 48 individuals. In my final VCF output almost all positions in these two Rattus rattus individuals is reported as ./. I checked using IGV and I find read coverage at all of those sites (avg coverage is around 15x) I have not applied any filter while calling the variants. Can you please help me understand why I am I seeing ./. for only these two samples?