How can I get the exon number/rank of a mutation from annovar annotation?
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4.9 years ago
liangqinsi ▴ 40

Dear all,

We want to get the exon number of a mutation like SnpEff's exon rank. But annovar's output seems have no such number. Is there some parameter or database I ignore?

Thanks

--- update command line ---

table_annovar.pl $vcf_dir/${sample}.vcf /Seq1/liangqinsi/anno_humandb/ -buildver hg19 -out $vcf_dir/${sample} -remove -protocol refGene,cytoBand,avsnp147,1000g2015aug_eas,1000g2015aug_all,clinvar_20160302,cosmic70,dbnsfp30a -operation g,r,f,f,f,f,f,f -nastring . -vcfinput

--- update solved ---

"-remove" will remove the temp file(*refGene.exonic_variant_function) which contains exon number.

And we can extract it from *hg19_multianno.vcf file. 囧

SNP sequencing annovar bioinfomatics annotation • 1.8k views
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Exon number is a non-unique identifier given that different transcripts will include or exclude different exons.

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Yes. We'll pick the transcript which contains all exon.

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The transcript you describe doesn't exist for each gene, you have mutually exclusive exons for example.

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"The preferred HGVS expression on a RefSeq cDNA. ClinVar does not report all HGVS expressions for each version of a RefSeq cDNA or each splice variant. There is a selection for what is reported and displayed, namely

a valid HGVS expression on the reference standard transcript defined by RefSeqGene, often calculated from a submission by ClinVar's automatic processing a valid HGVS expression on a cDNA from a submitter, even if the cDNA is not the reference standard transcript for RefSeqGene" You're right. In fact we pick the standard transcript as clinvar do.

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4.9 years ago
Zaag ▴ 800

http://annovar.openbioinformatics.org/en/latest/user-guide/gene/#output-file-2-refseq-gene-annotation

The second output file, ex1.exonic_variant_function, contains the amino acid changes as a result of the exonic variant. The exact format of the output below may change slightly between different versions of ANNOVAR.

This file also contains the exon number.

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Thanks Zaag, it help a lot..

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