Construction

In vg construct, we take a VCF file and the reference sequence it was based on and generate a variation graph suitable for use by other tools in vg. In the construction process we interpret the VCF+ref combination as a directed acyclic sequence graph. Variants in the input are decomposed using pairwise alignment between the reference and alternate, so that the input is interpreted as if it had been passed through vcfallelicprimitives.

The construction process can be distributed, as we'll construct the whole genome graph one chromosome at a time. We specify which chromosome we want to work on by giving vg construct the -R/--region parameter, which limits the constructed graph to a particular reference range. Any samtools-format region specifier will work, but here we'll use whole chromosomes. Presently, it's advisable to break the construction apart due to memory requirements of vg--- it is optimized for high performance mutable graphs, and stores them in memory in a very non-succinct way.

Now we make a file $i.vg for each chromosome $i:

ref=hs37d5.fa
vars=ALL.wgs.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz

echo constructing graph
(seq 1 22; echo X; echo Y) | parallel -j 24 "time vg construct -C -R {} -r $ref -v $vars -t 1 -m 32 >{}.vg"

This step should take about half an hour when using 24 cores. The result will be around 4.5G of .vg files, which are compressed protobufv3 defined by the vg format specification with a chunked on-disk format implemented by stream.hpp.