I generated VCF and .bam files from transcriptomes files of C.remanei. Now, I want to do some functional annotation of SNPs or some other analyses to begin with. I am actually very new to all these analyses and not sure what is the best way start with. I found some publications with usinf GWAS database but I am not sure if I could use it with C.remanei. Also, I found some information about VariantsToTable on GATK website but it looks like this tool makes only the table of all SNPs and do not perform functional annotation. All other functional annotations tools that I found ask about SNP IDs, which I do not have because there is no dbSNP file for C.remanei. Could you please advise what is the best way to start variants analyses with VCF and bam files?