Load data from a VCF file into numpy arrays

Posted: 22 February 2013 by Alistair Miles in Uncategorized

I’ve recently been doing some analysis of SNPs and indels from the MalariaGEN P. falciparum genetic crosses project, and have found it convenient to load variant call data from VCF files into numpy arrays to compute summary statistics, make plots, etc.

Attempt 1: vcfarray

I initially wrote a small Python library for loading the arrays based on the excellent PyVCF module. This works well but is a little slow, and when I profiled it it was the VCF parsing that was the bottleneck, so I went in search of a C/C++ library I could use from Cython…

Attempt 2: vcfnp

Erik Garrison’s vcflib library provides a nice C++ API for parsing a VCF file, so I had a go at writing a Cython module based on that. Performance is better, I get roughly 2-4X speed-up over the PyVCF-based implementation, although I was hoping for an order of magnitude … I guess it’s just the case that string parsing is relatively slow, even in C/C++, and we should be using BCF2.

To install and try vcfnp for yourself, do:

pip install vcfnp

See the vcfnp README for some examples of usage.

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