A complete gene desapears at gatk4 mutect2 bamout

[paumarc]

Good morning

i have been calling variants with mutect2 with minimal configuration; i just provided the bam file, the panel of normals and a bed, and my surprise was that a gene well covered at the original bam and with a variant that seemsipsbonhoollhola

I have been using to call variants with Mutect2. I am surprised that due to realignment done by mutect, almost a complete gene disappeared.

at the original bam, a recalibrated bam done by bwa using nf-core Sarek's pipeline, the gene btk seems well covered, and a SNP appears to being the normal nucleotide with 3372 reads (96%) and alternative nucleotide with 156 reads (4%)

this mutation is important for us, as it has diagnostic importance. It has been happening to us many times, and we are worried about it.

Can the realignment be ignored somehow?

thanks

a) GATK version used: Gatk4.6.20

b) Exact command used: normal comand with default parameters

gatk4-4.6.2.0--py310hdfd78af_0.sif gatk Mutect2
-R WholeGenomeFasta/genome.fa
-I 231309_PRE/231309_PRE.recal.bam -tumor 231309_PRE_231309_PRE
--germline-resource gemline_resources_path
--panel-of-normals $pon_path
--bam-output 231309_PRE/231309_PRE_multiple.recal.m2.bam
-O 231309_PRE/231309_PRE_maxread0.unfiltered.vcf.gz

i also tested other parameters as

--disable-read-filter MateOnSameContigOrNoMappedMateReadFilter
--force-active
--force-call-filtered-alleles
-emit-lod 0

c) Entire program log: