SNP annotation with ANNOVAR
Hi , i recently used ANNOVAR h19 to annotate SNPs . what i noticed that it didnt return the SIFT and Polyphen and MutationTaster for a large portion of exonic SNPs . for example this SNP :chr15-52233771-T-G . would be happy to know why, am I missing something? , I followed their guide when annotating my VCF . thank you
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which dataset is used ? I cannot see any hg19 exon using UCSC genome browser + gencode track, nor ucsc genes.
I used this command annotate_variation.pl -out ex1 -build hg19 example/ex1.avinput humandb/ but with my VCF as input and by default, --geneanno -dbtype refGene is assumed) -https://annovar.openbioinformatics.org/en/latest/user-guide/gene/