5.3 years ago by
If the .bam file was provided to you, then you might want to ask that company / core about analysis suggestions. There are many variant annotation programs (SeattleSNP, wANNOVAR, etc.) that are free on the web, but you'll need to call the variants first (using VarScan, GATK, etc.).
There was a paper recently published for STORMSeq:
It estimated the cost for processing a WGS sample to be ~$30, starting from the .fastq files and ending with the variant annotations..
Galaxy provides some NGS analysis tools (for free), but you'd probably want to use a local mirror (if possible). Otherwise, it will be very slow (and there may be a maximum time limit, I've never tried to use it for large datasets):