Genotyping for SNP

[Wangchangsh]

Hi,

Thanks for developing such wonderful tools. I failed in SNP genotyping. here are my materials and results:

candidates.vcf 
Chr1    178766    .    G       A       .       PASS    END=178766;ChrB=Chr1;StartB=178766;EndB=178766
Chr1    5244076 .        G       T       .       PASS    END=5244076;ChrB=Chr1;StartB=5244076;EndB=5244076
Chr1    5270928 .     A       C       .       PASS    END=5270928;ChrB=Chr1;StartB=5270928;EndB=5270928
Chr1    5271719 .     TTCAGCCATGGG    T       .       PASS    END=5271730;ChrB=Chr1;StartB=5271719;EndB=5271719
Chr1    5568692 .     T       C       .       PASS    END=5568692;ChrB=Chr1;StartB=5568692;EndB=5568692
Chr1    11462725       .  C       T       .       PASS    END=11462725;ChrB=Chr1;StartB=11462725;EndB=11462725

genotype result
GT:DP:FT:AD:ADF:ADR:PL  0/0:8:PASS:12,0:12,0:0,0:0,24,120
GT:DP:FT:AD:ADF:ADR     .:10:PASS,UNMATCHED:0,15:0,0:0,15
GT:DP:FT:AD:ADF:ADR     .:31:PASS,UNMATCHED:0,57:0,18:0,39
GT:DP:FT:AD:ADF:ADR     0/0:18:PASS:30,0:30,0:0,0
GT:DP:FT:AD:ADF:ADR     .:30:PASS,UNMATCHED:0,48:0,18:0,30
GT:DP:FT:AD:ADF:ADR     0/0:52:PASS:87,0:48,0:39,0

In IGV， I found the three sites Chr1:5244076, Chr1:5270928, and Chr1:5568692 should be "1/1", but the results were UNMATCHED.

Could you give me some advice? Thanks!

Sincerely,
Changsheng