Fwd: Problem with Annovar using Hg38

[Zayyad Siddiqui]

---------- Forwarded message ---------
From: Zayyad Siddiqui <zs...@virginia.edu>
Date: Mon, Nov 30, 2020 at 12:50 PM
Subject: Problem with Annovar using Hg38
To: <genom...@soe.ucsc.edu>

Hi I am trying to annotate vcf files to determine somatic variants for breast cancer. So I have the vcf files done. 

I have downloaded the proper databases using the slurm script here in my university's hpc:

However, when I try to use the table_annovar (line 15) to actually annotate the vcf file it gives an error saying that the file hg38_gnomad211 does not exist as seen here:

I tried downloading hg38_gnomad211_exome from your database website but have had no luck. Any ideas to resolve this? Thank you

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Best,

Zayyad Siddiqui

University of Virginia

Biomedical Engineering '21

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Best,

Zayyad Siddiqui

University of Virginia

Biomedical Engineering '21

[Luis Nassar]

Hello, Zayyad.

Thank you for your interest in the Genome Browser.

While we do offer GnomAD data for hg38, the specific file mentioned by table_annovar.pl is not one we offer. We are not overtly familiar with ANNOVAR, but it seems that the file is supposed to be created by the first script, annotate_variation.pl.

You may find better results contacting ANNOVAR or looking at the script's documentation, or perhaps asking your question in a general bioinformatics forum such as Biostars.

Let us know if you have any additional questions with regards to Genome Browser data or tools.

I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.

Lou Nassar
UCSC Genomics Institute

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