I've a question for those who've used the MiSeq Reporter program. In my lab we prepare a gene panel library (Agilent SureSelect QXT) and send it away to have it sequenced on a MiSeq by someone else. And my supervisor would like me to validate the gene panel according to the protocol his PhD student has developed. Her gene panel was made by Illumina and I don't know what downstream software they have, but she used the MiSeq Reporter and the Variant Studio software (Illumina). She used the MiSeq Reporter program to generate assay matrices and variant call files to look at mean coverage over all target regions and do some analysis on reproducibility and repeatability. I don't have the MiSeq Reporter program and I only get FastQ data files back from our sequencing people. I use the SureCall program to do analysis and I can generated QC reports with average coverage data and all of that.
From my understanding the FastQ files contain the raw data for each of my samples from the MiSeq run so the coverage data should be the same regardless of the program used? Or am I barking up the wrong tree?
My question is are the QCs the same from both programs? Do I need the MiSeq Reporter program to generate all this?