I also posted you your github issues. Basically the VCF has a this line:
NC_001136.10 410323 1755 A A . PASS Ty=SNP;Rk=0.073173;UL=77;UR=471;CL=.;CR=.;Genome=A;Sd=1 GT:DP:PL:AD:HQ 0/1:167:1138,17,1238:86,81:68,67 0/1:172:1427,21,1028:76,96:67,68
If I am interpreting that correctly then thats a SNP where REF is A and ALT is also A. Why is that called as SNP?