Question: ANNOVAR issue annotating vcf
0
gravatar for brismiller
5 months ago by
brismiller40
Bellingham, WA, USA
brismiller40 wrote:

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.

gnomad variant annover • 133 views
ADD COMMENTlink written 5 months ago by brismiller40
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