Bo

The procedure is generally run vtools select to create subset of variants and then vtools associate with the new variant table. How to select variants efficiently depends on your source...

Are you using python 3? If so, are you using the latest version from github? We recently fixed a python3 related issue (https://github.com/vatlab/VariantTools/issues/61).

The reason for the error message is that VST assumes hg19 because the variants will be resampled (evolved) from a thousand genomes data which is based on hg19. Your version...

Could you update your ticket with updated workflow and command line used?

Finally get some time to work on this and I can now reproduce the problem. I think this is a bug with tabix that has been [observed by others](https://github.com/grenaud/dice/blob/master/src/ReadTabix.cpp#L26).

I do not get it. ``` tabix ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz 22:18000000-20000000 ``` outputs the following as the first line ``` 22 17993930 esv3647221 T 100 PASS AC=1;AF=0.000199681;AN=5008;CIEND=-150,150;CIPOS=-150,150;CS=DEL_union;END=18000439;NS=2504;SVTYPE=DEL;DP=13526;EAS_AF=0;AMR_AF=0;AFR_AF=0.0008;EUR_AF=0;SAS_AF=0;VT=SV GT 0|0 0|0 0|0 0|0...

OK, I have pushed a patch to ignore loci that are extracted by tabix that are outside of the specified region. The workflow should work now.

This could significantly improve the performance of our `vtools update` operation on statistics, and filtering operations for `vtools associate`.

Please let us know the exact error messages you got. You should be able to load your data using option `--build hg19`.

Thanks. We will create databases such as minidbSNP for testing purposes later.