I am trying to call rare variants in pools of four tumor samples for a specific gene of interest. For that we did a amplicon next-generation sequencing on our pools. They all come tumor with a monosomy for the chromosome supporting our gene of interest.
I aligned the fastq files to the hg19 assembly using bwa mem and removed primers with BAMClipper (Au CH., 2017). I then take the union of three variant caller : Mutect2, HaplotypeCaller and Freebayes in single sample mode to call variants. A biological step of validation is made with Sanger sequencing for all potentially interesting variants.
The tools that I use take into parameter to call variants the ploidy of the pool (i.e for a pool of 8 germline DNA, the ploidy should be set to 16 - 8x2).
My question is the following : how should I adjust the ploidy parameter for pools of four monosomic tumor ?
My guess is that I should maybe increase the ploidy, and instead of setting it to 4 I should set it to 8 for instance because of the possible tumor contamination.
Does anyone have some thoughts or experience on cases like this ?