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WGLab / doc-ANNOVAR

Documentation for the ANNOVAR software
http://annovar.openbioinformatics.org
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annotate.variation.pl showing error #233

Open VISHUGUPTA-2712 opened 11 months ago

VISHUGUPTA-2712 commented 11 months ago

I am running a self made vcf file, and I am getting the following error when I am running table_annovar.pl command with refGene database. Please suggest where is the mistake?

Running system command <annotate_variation.pl -filter -dbtype refGene -buildver hg38 -outfile clinvar_result_annovar clinvar_result_annovar.avinput humandb/> NOTICE: the --dbtype refGene is assumed to be in generic ANNOVAR database format NOTICE: Output file with variants matching filtering criteria is written to clinvar_result_annovar.hg38_refGene_dropped, and output file with other variants is written to clinvar_result_annovar.hg38_refGene_filtered NOTICE: Processing next batch with 5 unique variants in 5 input lines NOTICE: Scanning filter database humandb/hg38_refGene.txt...Argument "chr1" isn't numeric in numeric eq (==) at ./annotate_variation.pl line 2603, line 1. Argument "NR_024540" isn't numeric in numeric eq (==) at ./annotate_variation.pl line 2603, line 1. Argument "chr1" isn't numeric in numeric eq (==) at ./annotate_variation.pl line 2603, line 2. Argument "NR_106918" isn't numeric in numeric eq (==) at ./annotate_variation.pl line 2603, line 2. Argument "chr1" isn't numeric in numeric eq (==) at ./annotate_variation.pl line 2603, line 3. Argument "NR_107062" isn't numeric in numeric eq (==) at ./annotate_variation.pl line 2603, line 3. Argument "chr1" isn't numeric in numeric eq (==) at ./annotate_variation.pl line 2603, line 4. Argument "NR_107063" isn't numeric in numeric eq (==) at ./annotate_variation.pl line 2603, line 4.