ANNOVAR issue annotating vcf
0
0
Entering edit mode
3.9 years ago
brismiller ▴ 50

Hey all, I am trying to annotate some wgs variant data with minor allele frequencies from the GNOMAD database. I am tring to use ANNOVAR to do this, but I am running into some errors.

executed:

annotate_variation.pl -regionanno -dbtype gnomad_genome -outfile test_out -buildver hg38 n4k_EGAF21.vcf humandb/

error:

NOTICE: Output file is written to test_out.hg38_gnomad_genome
NOTICE: Reading annotation database humandb/hg38_gnomad_genome.txt ... Error: invalid record found in region annotation database: <#Chr StartEnd    Ref Alt gnomAD_genome_ALL   gnomAD_genome_AFR   gnomAD_genome_AMR   gnomAD_genome_ASJ   gnomAD_genome_EAS   gnomAD_genome_FIN   gnomAD_genome_NFE   gnomAD_genome_OTH>

I downloaded the database following the instructions on the annovar website.

Any help on this would be appreciated, thanks.

annover variant gnomad • 1.0k views
ADD COMMENT

Login before adding your answer.

Traffic: 1180 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6