I have ran the Mutect2 with tumor only mode and get the VCF file, and then I check the mutation site in iGV with a bamout file and my raw bam file from bwa, but I have trouble in explain why Mutect2 only report one position while there are about 4 site obvious . mycode:
gatk Mutect2 -R $ref -I tumor.bam \ --germline-resouce af_genomAD.vcf.gz \ -bamout bamout.bam \ -O my.vcf.gz
I have follow the troubleshooting guide from GATK. Expected variant at a specific site was not called But it cannot explain this phenomenon well.
I want to know if anyone has the same problem, or there are some better explanations. This is the my raw bam file from bwa-mem. Thanks