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GATK 188.8.131.52 Mutect2 doesn't emit a real variant
Hello GATK team,
I have been trying the brand new Mutect2 v184.108.40.206 on ctDNA samples with high coverage. I noticed one case where Mutect2 v220.127.116.11 detected a variant, but the new version didn't even emit the mismatch.
Here is the original command I used:
gatk Mutect2 -R reference.fasta -I normal.bam \ -O variants.vcf.gz --germline-resource gnomadhg19.vcf.gz \ --panel-of-normals pon.vcf.gz -L targets.interval_list \ -ip 300 -normal normalSample -I tumor1.bam \ -I tumor2.bam -I tumor3.bam -I tumor4.bam
When I realized the missing variant, I reran Mutect2 with the following additional parameters, but that didn't help.
--force-active true --tumor-lod-to-emit 0 --initial-tumor-lod 0
Here is an IGV snapshot of the variant (it exists in only one tumor sample: Ref: 820, Alt: 29, N: 2)
The reads in the upper part are from the original bam and in the lower part from the bam file emitted by Mutect2
Thank you for your help