I am new to exome sequencing. I ran GATK4 and have a g.VCF file. I used VEP to annotate the gVCF file. I have a couple of questions.
- I noticed not all the rows(variants) have the CSQ flag. Is that normal? Or I missed something? [I used
--coding_onlyin VEP along with other options]
- What the main things to look for in a vcf file to get meaningful information out of the vcf file and what tools to use for that? [I don't have a specific list of genes to look for right now]