MuTect2 for amplicon did not call some variants

Hi GATK team,

I am a beginner for using GATK. I performed the amplicon-based target sequencing and then I used the GATK4-MuTect2 to call variants. However, when we compared the variants from GATK4-MuTect2 with those from VariantCaller on Ion Torrent Sever, we found some inconsistencies. Therefore, I generated the bamout and found that some variants seem to be realigned and therefore they did not be called (see figure chr17:50196078).

In other case, the allele frequency (AF) is homozygous in both input bam file and bamout, but the allele frequency (AF) is heterozygous in the vcf which is shown below and in the figure chr17:50188065.

chr17 50188065 . A G . clustered_events DP=6046;ECNT=18;POP_AF=5.000e-08;P_CONTAM=0.00;P_GERMLINE=-2.846e+01;TLOD=1518.06 GT:AD:AF:DP:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/1:447,1238:0.544:1685:174,937:273,301:32,36:0,0:60:12:0.737,0.525,0.735:0.00,1.00,0

The following is my parametric, IGV and VCF data,
date;/share/app/GATK/gatk-4.0.9.0/gatk --java-options "-Xmx256g" Mutect2 -R grch38.p2_rmsk.fasta -I 18060114.bam -tumor 18060114 -O 8060114_Mutect2_tumor_maxaf1_mrra0.vcf.gz --max-population-af 1 --max-reads-per-alignment-start 0 --min-base-quality-score 0

Your advise is highly appreciated, and look forward to your reply.

Thank you!

Respectfully yours,
Ching-Yuan Wang

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