If you are seeing an error, please provide(REQUIRED) :
a) GATK version used:
b) Exact command used:
c) Entire error log:

If not an error, choose a category for your question(REQUIRED):
a)How do I (......)?
b) What does (......) mean?
c) Why do I see (......)?
d) Where do I find (......)?
e) Will (......) be in future releases?

as seen below, the first sample "normal" has 6 ALTs but classified as 0/0, however, the secondary sample "tumor" has 0 ALT but classified as 0/1 and alternative allele frequency 0.020, why?

chr12 25380275 . T G . contamination;normal_artifact;weak_evidence AS_FilterStatus=weak_evidence,contamination;AS_SB_TABLE=79,82|3,3;DP=171;ECNT=1;GERMQ=93;MBQ=20,20;MFRL=142,141;MMQ=60,60;MPOS=16;NALOD=-7.887e+00;NLOD=2.99;POPAF=6.00;TLOD=-1.680e+00 GT:AD:AF:DP:F1R2:F2R1:SB 0/0:87,6:0.068:93:47,4:36,2:44,43,3,3 0/1:74,0:0.020:74:34,0:30,0:35,39,0,0

some additional information:

1) we called mutation with mutect2 in cancer only mode, and mutect2 found mutation in before-treatment but no mutation in after-treatment sample.

2) we then use before-treatment as "normal" and after-treatment sample as "tumor" as paired samples for mutect2 and expect to see mutation change. however, mutect2 by default setting did not call this mutation, we then used force-calls mode to call this mutation, as what I have described above, this output is not understandable !

I used gatk v4.2.2.0 and v4.1.8.1 and got the same result:

thanks for help!

If you are seeing an error, please provide(REQUIRED) :
a) GATK version used:
b) Exact command used:
c) Entire error log:

If not an error, choose a category for your question(REQUIRED):
a)How do I (......)?
b) What does (......) mean?
c) Why do I see (......)?
d) Where do I find (......)?
e) Will (......) be in future releases?