Hi,

I am using Mutect2 to call somatic variants. My command is 

gatk Mutect2 \
-R $genome_dir/genome.masked.fa \
-I $sample.sorted_marked.with_RG.bam \
-O $sample.mutect.vcf \
--germline-resource resources/af-only-gnomad.hg38.vcf.gz \
--panel-of-normals resources/1000g_pon.hg38.vcf.gz \
--af-of-alleles-not-in-resource 0.0000025 \
--tmp-dir . \
--QUIET true \
--verbosity ERROR \
--bam-output $sample.mutect2.bam

My version is:

The Genome Analysis Toolkit (GATK) v4.2.3.0
HTSJDK Version: 2.24.1
Picard Version: 2.25.4

I get weird INDELs which are not supported by the input bam file. In the bam file produced by Mutect2, multiple SNVs and INDELs are being introduced into the perfectly aligned region.

The example of the weird variants I'm getting in one of my samples: 

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 9272-PVG-0003
20 32434748 . G GTGCTCGGGCCTCCCCTGGGCTC . PASS AS_FilterStatus=SITE;AS_SB_TABLE=900,920|6,8;DP=1977;ECNT=3;GERMQ=93;MBQ=20,29;MFRL=168,157;MMQ=60,60;MPOS=19;POPAF=5.6;TLOD=19.61 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:1820,14:0.013:1834:480,2:455,3:1150,14:0|1:32434748_G_GTGCTCGGGCCTCCCCTGGGCTC:32434748:900,920,6,8
20 32434749 . A AGGGT . PASS AS_FilterStatus=SITE;AS_SB_TABLE=900,919|6,8;DP=1949;ECNT=3;GERMQ=93;MBQ=20,37;MFRL=168,157;MMQ=60,60;MPOS=18;POPAF=5.6;TLOD=19.82 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:1819,14:0.013:1833:471,3:447,3:1149,14:0|1:32434748_G_GTGCTCGGGCCTCCCCTGGGCTC:32434748:900,919,6,8

It looks like this in IGV (output/input files):

I would like to know the reason of this behaviour and how to prevent that.

Thanks!