I want to analyse missense de novo variants in context of autism spectrum disorder and I have access to already annotated (SnpEff) vcf files. Each VCF has at least a trio (father, mother, proband) and sometimes an unaffected sibling.
Do I need to phase before looking for de novo? Which tools can I use to do so? HaplotypeCaller for phasing and VariantAnnotator for de novo findings?
Is it also possible to get the SnpEff html report from an already annotated file?
And finally, what can I use to get an "nicer" output from a VCF file, to list every missense de novo, synonymous, ...