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WGLab / doc-ANNOVAR

Documentation for the ANNOVAR software
http://annovar.openbioinformatics.org
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Error for annotating chromosome and bp by rsID #250

Open ruuhsu opened 3 months ago

ruuhsu commented 3 months ago

Hello,

I recently encountered an error when trying to use 'convert2annovar.pl' to find CHR and POS by a list of rsID. The script I used showing below:

perl convert2annovar.pl -format rsid sID.txt -dbsnpfile humandb/hg38_avsnp151.txt > snplist.avinput

The error showing below: NOTICE: Scanning dbSNP file humandb/hg38_avsnp151.txt... Use of uninitialized value $class in string eq at convert2annovar.pl line 1048, line 1.

Wondering if there's an error in the convert2annovar.pl file. I made sure my rsID list in the same formate as the example rsID file.

Thank you!

wangwpi commented 1 month ago

Hi, you can try to use -avsnpfile instead of -dbsnpfile since you are searching the avsnp database. So the command could be: perl convert2annovar.pl -format rsid sID.txt -avsnpfile humandb/hg38_avsnp151.txt > snplist.avinput