Genome Diff to VCF function.

[GoogleCodeExporter]

Write a function that converts Breseq's Genome Diff format to VCF format. This 
format is useful for importing to IGV.

http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-cal
l-format-version-41

Make it a utility command, gd2vcf, in gdtools_cmdline.cpp for now.

Original issue reported on code.google.com by Geoffrey...@gmail.com on 12 Sep 2012 at 2:29

[GoogleCodeExporter]

I agree that having VCF output is crucial. We are developing a series of 
microbial tools in Galaxy (including our VelvetOptimiser etc) and BreSeq is 
looking like a good candidate to fill the variant calling role. These tools are 
for a national Australian project which we are part of, of which all will be 
freely available and include step by step instructions for beginners. But we 
need .VCF to integrate with the rest of Galaxy. PS. I agree VCF is a bit of a 
pain, especially needing context bases for indels! (makes it harder to write GD 
-> VCF wrapper)

Original comment by torsten....@gmail.com on 25 Dec 2012 at 9:03

[GoogleCodeExporter]

GD-format puts some thought into the results being human-readable, while VCF 
makes you do some thinking. If you look into the evidence output in GD-format 
you'll see that it's not far off from VCF. 

What microbes are being studied and what types of structural variants are you 
hoping to predict with Breseq?

Original comment by Geoffrey...@gmail.com on 27 Dec 2012 at 4:40

[GoogleCodeExporter]

We should have a way to at least convert our genome diffs fully to VCF format, 
especially now that VCF 4.0 now has some ways of putting structural variants in

http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/VCF%20(Variant%
20Call%20Format)%20version%204.0/encoding-structural-variants

It still loses the evidence to mutation mapping... and the idea of mutations 
that can be applied as events, rather than that we are counting variants. So, 
some further thought is required.

Original comment by jeffrey....@gmail.com on 11 Jul 2013 at 9:26

[GoogleCodeExporter]

There is basic VCF output available now via the "gdtools GD2VCF" conversion now 
in v0.24*

Original comment by jeffrey....@gmail.com on 8 Aug 2014 at 9:38

• Changed state: Fixed