What is the difference between the manta disease model (--tumorBam) and germline model (--bam)? i.e, different calling algorithms, different filtering criteria? Is there some detailed documentation on that?
The short answer is that the germline model assumes a diploid sample with corresponding allele frequencies. The tumor-only model assumes the variant could occur at any allele frequency. The best starting point for a high-level overview is the user guide: