I am new to bioinformatics. so this may be silly question.
We would like to do Pharmacogenomics clinical decision support. Instead of using genotyping, we want to use whole genome sequencing. I am assuming we will send 8 patient samples for analysis. (ideally we wound sent just one, but the pricing is such that we have to send a batch). There are lots of format and it is hard to know where to start, what we will have to do in-house and what can we get our of the box (going only to sequencing vendor, not interpretation vendor)
My questions are:
in what format we can expect to get the raw data? (would that be fastaq or BAM/SAM)
does one get right away a *.vcf file from a vendor or we will have to process it ourselves? (against which reference genome it would be done - would that be Homo sapiens GRCh37 Primary Assembly?