SNP/SNV effect and annotation
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1 SNP/SNV effect and annotation Laurent Falquet, Oct 18 Why annotating the SNVs? Annotate the function of a mutation (change or the effect of a variant) Restrict the space of search Ultimate goal: allow identification of causative mutation (link phenotype and genotype)
2 Potential effects depends on the location of the SNV In coding regions SYNONYMOUS (SILENT) MISSENSE NONSENSE (STOP GAINED) STOP LOST START LOST IN FRAME INSERTION OR DELETION FRAMESHIFT... many other S -> S S -> R S -> * * -> S M -> K S -> SA or S -> - S -> F
3 Some tools for coding regions SNPeff/SNPsift ENSEMBL Variant Effect Predictor (VEP) ANNOVAR java -jar snpeff.jar databases grep cerevisiae EF4.71 Saccharomyces_cerevisiae EF4.72 Saccharomyces_cerevisiae EF4.73 Saccharomyces_cerevisiae EF4.74 Saccharomyces_cerevisiae R Saccharomyces_cerevisiae R Saccharomyces_cerevisiae R Saccharomyces_cerevisiae R Saccharomyces_cerevisiae R Saccharomyces_cerevisiae R Saccharomyces_cerevisiae R Saccharomyces_cerevisiae R Saccharomyces_cerevisiae OK R Saccharomyces_cerevisiae java -jar snpeff.jar download v R
4 Run snpeff Execute the command with SGE: java -Xmx20g jar snpeff.jar -classic \ -no-upstream -no-downstream R \ variant.flt.vcf > variant.flt.annot.vcf Example: EFF=STOP_GAINED(HIGH NONSENSE tac/tag Y4* 407 NIS1 protein_coding CODING YNL078W 1 1) EFF=NON_SYNONYMOUS_CODING(MODERATE MISSENSE Gct/Act A191T 458 SSU1 protein_coding CODING YPL092W 1 1) EFF=SYNONYMOUS_CODING(LOW SILENT aca/act T FLO9 protein_coding CODING YAL063C 1 1) EFF=INTERGENIC(MODIFIER 1) This command also generates 2 statistics files: snpeff_summary.html (overall statistics) snpeff_genes.txt (for each gene)
5 ENSEMBL VEP
6 ENSEMBL VEP results ENSEMBL VEP results
7 Tools to predict functional impact of a variant in Human proteins SIFT ( PROVEAN ( PolyPhen2 ( MutationAssessor ( they do not agree Condel/TransFIC as a combined tool ( Tools annotating variants in non-coding regions phastcons uses a database of conserved elements in vertebrates GERP++ identifies constrained elements in multiple alignments by quantifying substitution deficits
8 SNV catalogues (mainly for Human) 1000genomes dbsnp HAPMAP ENSEMBL GWAS central dbnsfp SNP effect with VEP Try loading your vcf file to the VEP tool Click: New job Select genome: Saccharomyces cerevisiae Select input format: vcf Upload your vcf file Click: return results for variants in coding regions only Click: Run Do you see identical results?
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