Annotate VCF with gene names

Im trying to add annotations to a vcf file.
I had paired-end reads of 3 individuals, I aligned each pair to the human hg19 genome, then I generated the VCF file using FreeBayes to call for variants of the 3 sets of data, then i wanted to annotate these variants using ANNOVAR Annotate VCF.
the output was:
“0 lines
WARNING to old ANNOVAR users: this program no longer does line-to-line conversion for multi-sample VCF files. If you want to include all variants in output, use ‘-format vcf4old’ instead.
NOTICE: Finished reading 2497 lines from VCF file
NOTICE: A total”
I did this previously on a VCF file with a single set of data (1 sample) and it worked fine. I looked up the help forum, and then found an advice to split the samples and then run ANNOVAR tool. I split the samples using VCFselectsamples tool and then when I ran the Annovar on these single-sample files I obtained a file with no data (0 lines & 0bytes) for each.
I have to point out that I re-ran the annovar tool step I used before (which worked fine) and it gave me 0 lines as well!! so does this mean ANNOVAR is down? I was also looking for alternative tools, but they all look very complicated and Im still a beginner.

So could someone support me with this issue? how can I get the task of annotating VCF done? I mean it should be straight forward but I spent 2 whole days reading forums and trying things and still getting no success.

Thanks in advance,

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I am using public galaxy if that info is relevant

Hello @yahia.elshabrawy

Yes, Annovar at is currently non-functional. The tool will likely be deprecated:

Alternative VCF annotation tools can be found in the tool grouping “Variant Calling”. SnpEff is one example.

GTN Tutorials may help with usage and creating a workflow. Start with those under the topic “Variant Analysis”.

Hope that helps!

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Thank you very much!!

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