I have a question about the Mutectcaller (Parabricks accelerated) version 4.0.0-2 on UK Biobank Research Analysis Platform.
In my project, I’d like to do somatic variant calling of SNPs and INDELs with the UKB WES data using the Mutectcaller (Parabricks accelerated) on RAP. I’d like to run somatic variant calling using the Mutectcaller tool in tumor-only mode with a panel of normals (PON).
Is Parabricks Mutectcaller from version 4.0.0.-2 support Panel of Normals to process variants? If yes, How to run this tool tumor-only mode with a panel of normals (PON)? I read this section in the documentation.https://docs.nvidia.com/clara/parabricks/4.0.0/documentation/tooldocs/man_mutectcaller.html#man-mutectcaller
As far as I understand, Firstly I should creat the input.pon and then I should run this tool in tumor-only mode with using input.pon file. If that is the case I have 2 questions.
Question 1: When I run this tool using sample of normal BAMs/CRAMs, I will not get just one output VCF file. Because this tool is just to convert to VCF, not merge. This being the case, How can I create the input.pon?
Question 2: Let’s assume that I was able create input.pon file, How will I select the VCF as input?
This tool only accepts these file as input;
ref file .bwa-index.tar.gz
interval file .bed
tumor recal file
normal recal file
Thank you very much in advance for helps.