Awesome

tdb: Tandem repeat database and analysis queries

Installation

git clone https://github.com/ACEnglish/tdb.git
cd tdb/
python3 -m pip install . 

Quick Start

Convert a tdb compatible VCF and run a query with:

tdb create -o output.tdb input.vcf.gz
tdb query allele_cnts output.tdb

Merge samples with:

tdb merge --output merged.tdb --mem 20 --threads 4 output1.tdb output2.tdb

Recommended 5-10GB of memory per-thread

Merge more samples into a tdb with:

tdb merge --into merged.tdb output3.tdb output4.tdb ...

For merging ≥10 tdbs, use:

tdb bigmerge -o merged.tdb results/samples*.tdb

Tutorials

See the wiki for details on what tdb is or jump straight into making your own custom tdb queries with notebooks/Introduction.ipynb.