kaichop
commented
2 years ago If there is a GA deletion, then the alternative allele should be "-" in ANNOVAR input format. Alternatively, you can always use VCF files, and use table_annovar (-vcfinput), if the VCF file has the correct alternative allele listed. I am very much against the whole concept of either using rs identifier to represent a mutation (which is incorrect), or use '*' to represent an unidentifiable deletion that may or may not be two bases, or to put multiallelic variant on the same line of VCF file. If you already know what the ALT is, you could manually put it in the VCF file before annotation.
On Fri, Apr 8, 2022 at 2:50 AM Karthik Nair @.***> wrote:
Hello,
According to this post by GATK https://gatk.broadinstitute.org/hc/en-us/articles/360035531912-Spanning-or-overlapping-deletions-allele-,
- in ALT field can indicate that the variant spans a deletion. When annotating such variants with annovar, I noticed that the * were interpreted as 0.
While annotating with Clinvar database, it wrongly identified the input and matched to different variant in the same loci - Our variant - chr19 15547993 15547994 GA 0
The Clinvar variant it matched to - rs71176433 https://www.ncbi.nlm.nih.gov/snp/rs71176433
Please note how our reported variant is a GA deletion, while the deletion in clinvar spans multiple nucleotides delAGGG(AG)3(TG)5
What could be the reason for this discrepancy and how to resolve it?
I can think of replacing the 0 in avinput to - which would make it in line with annovar convention, would that be worth a shot?
Thanks for your time!
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nurmians
Hello,
According to this post by GATK,
*in ALT field can indicate that the variant spans a deletion. When annotating such variants with annovar, I noticed that the*were interpreted as0.While annotating with Clinvar database, it wrongly identified the input and matched to different variant in the same loci - Our variant -
chr19 15547993 15547994 GA 0The Clinvar variant it matched to - rs71176433
Please note how our reported variant is a
GAdeletion, while the deletion in clinvar spans multiple nucleotidesdelAGGG(AG)3(TG)5What could be the reason for this discrepancy and how to resolve it?
I can think of replacing the
0in avinput to-which would make it in line with annovar convention, would that be worth a shot?Thanks for your time!