Hi!

I'm trying to find mutations in tumor samples. Sample was sequencing on a gene panel. Everything is going well in my pipeline up to the Mutect2 stage. Before starting the Mutect2, my sample has very good depth coverage. But after Mutect2 in vcf file there are sap with DP=3 or less

I check the found SNP in the program and confirm that in the initial bam this position has a coverage of more than 20

There is my code in snakemake format:

    rule gatk_Mutect2:
            input: bed="out_intersect_bed/{bed}.bed", ref="hg38/ref.fa", bam="srr11097713_1_base_recalibrate.bam", gnomad="af-only-gnomad.hg38.vcf.gz"
            output: vcf="out_Mutect2/srr11097713.mutect2.{bed}.vcf",  f1r2="out_Mutect2/srr11097713.{bed}.f1r2.tar.gz"
            shell: "gatk-4.2.4.1/gatk --java-options ""-Xmx7680m""  Mutect2 -L {input.bed} -R {input.ref} -I {input.bam} -tumor TUMOR --germline-resource {input.gnomad} -O {output.vcf}
 --f1r2-tar-gz {output.f1r2} --create-output-bam-index false

VCF looks like this:

##filtering_status=Warning: unfiltered Mutect 2 calls.  Please run FilterMutectCalls to remove false positives.
##source=Mutect2
##tumor_sample=TUMOR
#CHROM    POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  TUMOR
chr3  37025867    .   G   A   .   .   AS_SB_TABLE=0,0|0,0;DP=1;ECNT=1;MBQ=0,29;MFRL=0,283;MMQ=60,60;MPOS=10;POPAF=7.30;TLOD=3.08  GT:AD:AF:DP:F1R2:F2R1:FAD:SB    0/1:0,1:0.667:1:0,0:0,1:0,1:0,0,1,0