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Mutect2 Somatic mutation genotype is not like HaplotypeCaller genotype
I use mutect2 (version 3.7) to detect somatic mutation, got the result, but I find the GT is not like HaplotypeCaller。
such as 0/1:0,77 ,genotype is 0/1, and ref depth is 0 , alt depth is 77 , in HaplotyeCaller the gentoype should be 1/1.
I am a bit confused , is the rule different between somatic and HaplotyeCaller ?
I have another question, can I identify germline mutation in mutect result ? like the flag "germline_risk" , is it accurate?
Maybe I detect germline mutation by use HaplotyeCaller again ?
chr1 3422642 rs2247236 A G . PASS DB;ECNT=1;HCNT=2;MAX_ED=.;MIN_ED=.;NLOD=18.92;TLOD=227.68 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/1:0,77:1.00:43:34:0.442:0,2708:0:0 0/0:87,0:0.00:0:0:.:3376,0:41:46