Closed davidhoover closed 3 years ago
When running SnpSift, I ran into this error:
“Exception in thread “main” java.lang.RuntimeException: Cannot parse EffectType ‘transcript’
I pinned down the error to the second term of an annotation block:
ANN=G|........,G|transcript|MODIFIER|TMEM240|ENSG00000205090|transcript|ENST00000425828|proteincoding||c.-9-2-7delGGCCC||||||; .......
If I substitute 'transcript' in the second field to something else (e.g. gene_variant), SnpSift has no problems.
The VCF input was annotated using SnpEff:
java -jar $SNPEFF_JAR -c $SNPEFF_HOME/snpEff.config -v -canon -no-intergenic -no INTRAGENIC -no-downstream -no-upstream -no-utr -no PROTEIN_STRUCTURAL_INTERACTION_LOCUS -no NEXT_PROT -noStats GRCh37.75 ../test.vcf
Closing old issues.
pcingola
commented
3 years ago pcingola
commented
3 years ago
When running SnpSift, I ran into this error:
“Exception in thread “main” java.lang.RuntimeException: Cannot parse EffectType ‘transcript’
I pinned down the error to the second term of an annotation block:
ANN=G|........,G|transcript|MODIFIER|TMEM240|ENSG00000205090|transcript|ENST00000425828|proteincoding||c.-9-2-7delGGCCC||||||; .......
If I substitute 'transcript' in the second field to something else (e.g. gene_variant), SnpSift has no problems.
The VCF input was annotated using SnpEff:
java -jar $SNPEFF_JAR -c $SNPEFF_HOME/snpEff.config -v -canon -no-intergenic -no INTRAGENIC -no-downstream -no-upstream -no-utr -no PROTEIN_STRUCTURAL_INTERACTION_LOCUS -no NEXT_PROT -noStats GRCh37.75 ../test.vcf