Thanks Zaag, it help a lot..
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liangqinsi •
How can I get the exon number/rank of a mutation from annovar annotation?
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.
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Ram
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liangqinsi •
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liangqinsi •
1 answer
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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Exon number is a non-unique identifier given that different transcripts will include or exclude different exons.
Yes. We'll pick the transcript which contains all exon.
The transcript you describe doesn't exist for each gene, you have mutually exclusive exons for example.
"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.