svaha - generate variation graphs for structural variants.

Make variation graphs from structural variants:
[x] Deletions [x] Inversions [x] Insertions [x] SNPs [ ] Duplications [ ] Transversions [ ] Breakpoints

Don't worry: we'll be adding these as time permits.

What is svaha?

svaha is a small program that converts Variant Call Format (VCF) records into Graphical Fragment Assembly format (i.e. sequence graphs like those in vg). It does so using a minimal single-base graph representation, the world's smallest and least-safe VCF parser (well, probably), and almost no dependencies.

Build it

svaha brings in its own libraries, except for zlib. Make sure to have zlib installed. It uses a frozen version of htslib and floating versions of gfakluge. To build svaha:

            git clone --recursive https://github.com/edawson/svaha
            make

and that should do it.

Run svaha

svaha takes a FASTA file and a VCF as arguments:
./svaha -r MYFASTA.fa -v MYVARIATION.vcf

and outputs sorted GFA, which is text-based and easily exchangeable to other, more useful programs (like vg).

Options

-r: a fasta reference
-v: a vcf containing variants (must be relative to the given fasta)
-m: maximum node size. When creating graphs for vg, make sure to use a maximum node size of between 32 and 1023.
1023 is a hard limit (nothing 1024 or over will be indexable) and below 32 the graph begins to eat tons of memory. I tend to use -m 64 or -m 128.

Workflows

1. Build a variation graph with svaha containing structural variants
2. Reduce node size with a cat result.gfa | vg view -F -v - | vg mod -X 1000 - > new_graph.vg to make the resulting graph indexable with GCSA2.
3. Map reads to that graph using vg map
4. Call variants using vg call or vg genotype

Get help

Reach out to me (@edawson) on GitHub and I'll do my best to help!