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annotate.variation.pl showing error #233

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VISHUGUPTA-2712 opened this issue Oct 27, 2023 · 0 comments
Open

annotate.variation.pl showing error #233

VISHUGUPTA-2712 opened this issue Oct 27, 2023 · 0 comments

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@VISHUGUPTA-2712
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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.

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