I am using a regular vcf file as input for the ANNOVAR Annotate VCF tool. Note that I use Galaxy public server. Using "edit attributes" I set hg19Patch10 as reference genome of the vcf file.
ANNOVAR accepts the input file but as output it returns an empty tabular file with the message:
format: tabular, database: hg19Patch10
Log: tool progress Log: tool progress NOTICE: Finished reading 783 lines from VCF file NOTICE: A total of 725 locus in VCF file passed QC threshold, representing 625 SNPs (443 transitions and 182 transversions) and 121 indels/substitutions NOTICE: Finish
Why am I getting an empty tabular file?
Do I need to install ANNOVAR or use Tool Shed with a cloud or local Galaxy (as mentioned in this post: https://biostar.usegalaxy.org/p/8508/ ) in order to get the results? And does this include the option to use mouse reference genome for different vcf files?
I must also note that I am using a vcf file with only one sample.