I've implemented a somatic variant calling pipeline in order to detect somatic variants in ovaric tumour samples (Targeted Sequencing done by MiSeq, Illumina). I now need to validate this pipeline; at this aim I'd like to know which are the best datasets to use in order to benchmark. Moreover, in order to evaluate the perfomances of my pipeline against other pipelines which are the best metrics to calculate and compare ? Which tool shall I use to compare the performances of 2 different variant calling pipelines (so to compare 2 different VCF files)?
Thanks in advance