Bo

Did you try to set `encoding` in your `.ann` file as documented [here](https://vatlab.github.io/vat-docs/applications/annotation/customized/)?

Ok. I will have a look today. Could you send me your .ann file?

Thanks. It will take a few days though because it is very time consuming to create large databases in sqlite and build indexes will take even longer.

Just download the data and tried your annotation file and noticed a bunch of ``` WARNING: hg19: Inconsistent base allele A at 114358819 on chromosome 2 ``` As far as...

Assuming v4 has the correct index for hg19, you could create an `.ann` file with only the fields you need, which will result in MUCH faster build speed and much...

I have notified the maintainer of [this annotation database](https://github.com/vatlab/VariantTools/blob/master/annotation/ExAC.ann) but he might not be able to update it in the next few days because of a deadline. If ExAC has...

@gaow Any quick thought on this?

The "dump data" association method is the `GroupWrite` method described [here](https://vatlab.github.io/vat-docs/applications/association/basic_data_statistics/group_stat_write/). It does not accept `NA` filtering though. @jma7 How difficult it is to support the filtering parameters for `GroupWrite`?

Yes, this will allow the user to reproduce the behavior of other tests that use such filters.

Sorry that I did not notice this ticket till today. What version of Python are you using?