Bo

Changing ``` export_by=chr,%(pos)s,%(ref)s ``` to ``` export_by=chr,%(pos)s,%(ref)s,%(alt)s ``` in `vcf.fmt` ``` [format description] description=Import vcf variant=chr,%(pos)s,%(ref)s,%(alt)s genotype=%(geno)s variant_info=%(var_info)s genotype_info=%(geno_info)s # variants with identical chr,pos,ref will be collapsed. export_by=chr,%(pos)s,%(ref)s ``` should...

@brankovicmarija Could you send us a minimal example to demonstrate the problem, such as the first 1000 lines of your vcf file and exact commands that you have used?

OK, let us disable the entire test_associate for now.

Do you by any chance still have the data (partial) and code to reproduce the problem?

This is perhaps because dbNSFP does not have any indels, so you probably want to use `vtools exclude` with a negative condition.

There is an example on [export doc](http://varianttools.sourceforge.net/Vtools/Export#toc6) on how to export genotype info. The command used was ``` % vtools export variant --samples 'sample_name like "NA128%"'\ --geno_info DP_geno --format_string 'GT:DP'...

This looks like a bug. I will have a look.

Could you send me the exact command for your *do an output*? It would be best if you could send me, even in private email, a sample vcf file and...

In sqlite, the rows are removed.

There is a way to remove the readme and java files, but for convenience, I would suggest that you unpack the zip file to a directory, remove all unnecessary files,...