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A bug in snp results from Haplotyper

I took use Haplotyper to get snp.vcf results.

There 's a snp is strange:

chr2 29448423 . T G 299.77 PASS AC=1;AF=0.500;AN=2;DP=114;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.80;MQ0=0;QD=2.63 GT:AD:GQ:PL 0/1:114,0:99:328,0,13034

Both DP and AD are 114;

Depth of reference is also 114.

Isn't this position 0/0 ?

Is this a bug for Haplotyper ?

I checked bam files and found that there were 119 reads covering this position.

114 for T
5 for G

Why is the information of these 5 reads supporting G missing?

Thank you ~


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