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6.5 years ago
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Hello,
We are using annovar to annotate our NGS gene panel that has both exonic and intronic variants. It works fine for most of it but does not give the correct HGVS annotation for intronic indels.
So for example, we have a variant
chr9:35061693 rs11272867 G GACAGTACACAA
The HGVS annotation should be NM_007126.3:c.1082-18_1082-8dupTTGTGTACTGT
But annovar annotates it as NM_007126.3:exon10:c.1082-7->TTGTGTACTGT which is incorrect
The commands I follow are
perl convert2annovar.pl --format vcf4 final.vcf --withzyg --includeinfo > final.ann
perl table_annovar.pl final.ann humandb/ --buildver hg19 --protocol refGeneWithVer,gnomad_exome,snp138 --remove --otherinfo --operation g,f,f --nastring - --out results
The table annovar script has only the following edits
"annotate_variation.pl -geneanno -buildver $buildver -hgvs -dbtype $protocol -outfile $tempfile.$protocol -exonsort -separate -exonicsplicing -splicing_threshold 30 $queryfile $dbloc"
has anyone encountered similar issues with HGVS annotations ?
Thank you,
Yes Annovar is not good for HGVS. Try VEP or SnpEff
Thanks @Jeremy With SNPEff, is there a way to have the output in a tab delimited file as it would be easier to extract certain annotated columns of interest ?
there might be some debug-level support for tabular output in snpeff but it doesn't make much sense in real life b/c of the one-to-many nature of variants-transcripts-effects
Duplications are insertions except that inserted bases are identical to bases next to the duplication event. Probably annovar is annotating it as insertion instead of duplication.
yes but the HGVS annotation coming from annovar is in incorrect format either way