I am performing somatic variant calling on NGS data (NGS targeted sequencing performed with Illumina MiSeq) using Mutect2. I do not have the normal match, so I am performing Mutect2 only on tumor samples. The result is a very high number of variant calls which makes me think there's something wrong. So how can I solve this problem? Are there any filtering steps I must perform (I have already performed FilterMutectCalls) ?
Thanks in advance.