Error for annotating chromosome and bp by rsID

[ruuhsu]

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]

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