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Stop combining variants in `vtools export`

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I have those two variants in my vtools variant database: ``` 4 106156653 T C Scan1,Scan2 ....,.,.,.,.... 4 106156653 T G Scan1,Scan2 ....,.,.,.,.... ``` So, when I export it to...

Variant Simulation Tools is a component of VariantTools that focuses on the simulation of genetic variants. It relies on Variant Pipeline Tools so it got broken with the deprecation of...

vtools remove variants does not work for hdf5

2

The syntax is `vtools remove variants TABLE` where `TABLE` is a variant table. In sqlite, the implementation is something like ([code](https://github.com/vatlab/VariantTools/blob/v3/src/variant_tools/project.py#L2280)] ``` DELETE FROM genotype_2 WHERE variant_id IN (SELECT variant_id...

vtools remove genotype does not work for hdf5

2

This one is even more difficult than remove variant because we are using a condition on genotype fields to remove genotype ([code](https://github.com/vatlab/VariantTools/blob/v3/src/variant_tools/project.py#L2296)). The query is something like ``` DELETE FROM...

This thread is used to update the implementation of the HDF5 storage model. ### Pending * `init`: * `--store` added to allow specification of storage model. * `--parent` and `--children`...

Sample tables are merged in command `vtools admin merge-samples`.

Problem with vtools select

1

I have been using Variant Tools to annotate damaging variants with dbNSFP (please see below the command I used). I noticed that none of the frameshift insertions and deletions remained...

How to export FORMAT fields in vcf format

3

I have been running the vtools on vcf file containing 3 WES samples (after GATK) Command: 1. I have used the import : ``` vtools import ../../../align/recalibrated_variants_.vcf --var_info DP filter...

Tests too large for travisCI

2

Downloading reference genomes hg18 and hg19 might be unavoidable but downloading hg19 is too much. We should remove some tests that require large resources.

Moved from https://github.com/vatlab/vat-dp/issues/11 1. It is not sparse for simple scenarios (where genotypes are coded 0/1/2/NA) 2. It does not distinguish between 0 and NA, unless we specifically asks it...