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WGLab / InterVar

A bioinformatics software tool for clinical interpretation of genetic variants by the 2015 ACMG-AMP guideline
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Intervar Database not available for download #28

Open GerardTromp opened 6 years ago

GerardTromp commented 6 years ago

Hi,

First, thanks for all the hard work.

When I try to download the InterVar database using: ./annotate_variation.pl -build hg19 -downdb intervar_20180118 humandb/

the screen output is (no logfile written). NOTICE: Web-based checking to see whether ANNOVAR new version is available ... Done NOTICE: Downloading annotation database http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/intervar_20180118.txt.gz ... Failed WARNING: Some files cannot be downloaded, including http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/intervar_20180118.txt.gz

I visited the UCSC web page, and indeed, there is no intervar file at all (i.e., no variant by date).

Since the instructions to download intervar are on the ANNOVAR site, I am reporting this here so that ir might be useful to others.

I have sent e-mail with the same information

kaichop commented 6 years ago

This is an ANNOVAR database and you should NOT use it for Intervar (it is useful for ANNOVAR users for a quick-and-dirty analysis of a subset of missense mutations).

If you truly want to use InterVar, follow instructions step by step. Forget about this file.

If you want to use annovar only to get some quick results and do not care about indels, etc, then read FAQ #3 in ANNOVAR website.

On Fri, Apr 13, 2018 at 1:15 AM, Gerard Tromp notifications@github.com wrote:

Hi,

First, thanks for all the hard work.

When I try to download the InterVar database using: ./annotate_variation.pl -build hg19 -downdb intervar_20180118 humandb/

the screen output is (no logfile written). NOTICE: Web-based checking to see whether ANNOVAR new version is available ... Done NOTICE: Downloading annotation database http://hgdownload.cse.ucsc. edu/goldenPath/hg19/database/intervar_20180118.txt.gz ... Failed WARNING: Some files cannot be downloaded, including http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/ intervar_20180118.txt.gz

I visited the UCSC web page, and indeed, there is no intervar file at all (i.e., no variant by date).

Since the instructions to download intervar are on the ANNOVAR site, I am reporting this here so that ir might be useful to others.

I have sent e-mail with the same information

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/WGLab/InterVar/issues/28, or mute the thread https://github.com/notifications/unsubscribe-auth/AFptuCOFI6TgMtxwfoKPBofWiILsntdIks5toDRdgaJpZM4TS3RE .