I’m a microbiologist with limited computational/bioinformatic training ( but can hack it when necessary with prokaryotic genomes). However, I recently was given a committee position within an AKC dog breed club and have found 8 whole genome sequences related to a breed-specific genetic disease that were not being worked up due to personnel time constraints (they focused on a GWAS).
I was given FASTQ files for the 8 dogs, 4 healthy and 4 diseased, all run on the same Illumina HiSeq flow cell. The disease is not cancer.
Any suggestions on what general steps to take to even have a shot at aliments would be great. Even if I can just formulate a plan that we can present to a computational person at some point that would be a big step. I assume I want to do some sort of aliment of the 4 healthy and 4 diseased in order to generate SNP, mobile element and CNV pileups. The only canine-specific platform I could find was CANFAM3.1, which doesn’t seem to allow for WGS alignments, just mapping of a single set of reads to the ‘stock’ canine genome, or checking what a gene may be involved in.