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Old 09-16-2014, 11:10 AM   #1
satishkumar
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Location: Asheville

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Default Variant annotation- uanble to get HGVS Nomenclature for intronic region

Hello All,

I am trying to annotate my variants. I am finding it hard to annotate my intronic regions (+/- 10bp from the exonic region). I am currently using Annovar to annotate them.

Any suggestion of how to tweak the parameter to get that regions annotated or link to the HGV nomenclature information corresponding to the NM number will be useful.

Thanks,

Satish
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Old 09-16-2014, 01:45 PM   #2
Bukowski
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The annotation is 'intronic' in this case then surely?

HGVS nomenclature can be anchored against a genomic coordinate if you want, but there are guidelines for intron naming. However there are multiple ways to describe an intronic variant and the tools I use certainly wont assign HGVS nomenclature to intronic variants.

http://www.hgvs.org/mutnomen/recs-DNA.html

Quote:
intronic nucleotides (coding DNA reference sequence only)
beginning of the intron; the number of the last nucleotide of the preceding exon, a plus sign and the position in the intron, like c.77+1G, c.77+2T, ....
end of the intron; the number of the first nucleotide of the following exon, a minus sign and the position upstream in the intron, like ..., c.78-2A, c.78-1G.
in the middle of the intron, numbering changes from "c.77+.." to "c.78-.."; for introns with an uneven number of nucleotides the central nucleotide is the last described with a "+" (see Discussion)
NOTE: the format c.IVS1+1G and c.IVS1-2G should not be used (see Discussion)
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Old 09-17-2014, 04:59 AM   #3
girlmonkey
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Hi, I believe with ANNOVAR you have to set -splicing_threshold to the value required to annotate intronic variants (by default it is 2) - so for example '-splicing_threshold 10' in your case might work.
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Old 10-09-2014, 08:56 PM   #4
reece
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We recently released and published our HGVS Python library for parsing, formatting, mapping, and validating variants.

http://bioinformatics.oxfordjournals...tu630.abstract

A major advantage of the library over other options is that the code correctly handles diabolical cases where the reference-transcript alignment contains indels (affects ~460 genes). The package extensively tested with manually mapped variants and against dbSNP and Mutalyzer. (The only discrepancies with Mutalyzer were in genes where there were alignment indels.)

I recently implemented experimental support for adding HGVS tags to VCF files. See https://bitbucket.org/hgvs/hgvs/issu...-hgvs-variants.
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