Question: HGVS annotation for intronic indels with annovar
0
gravatar for Nandini
17 months ago by
Nandini780
London
Nandini780 wrote:

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,

intronic indels annotation hgvs • 1.2k views
ADD COMMENTlink written 17 months ago by Nandini780
1

Yes Annovar is not good for HGVS. Try VEP or SnpEff

ADD REPLYlink modified 17 months ago • written 17 months ago by Jeremy Leipzig18k

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 ?

ADD REPLYlink modified 17 months ago • written 17 months ago by Nandini780

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

ADD REPLYlink written 17 months ago by Jeremy Leipzig18k

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.

ADD REPLYlink modified 17 months ago • written 17 months ago by cpad011211k

yes but the HGVS annotation coming from annovar is in incorrect format either way

ADD REPLYlink written 17 months ago by Nandini780
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