Genes for Good

[pvjones]

Hey, do you have any interest in adding a parser for Genes for Good? It's a group at University of Michigan that offers free genotyping.

They provide users with text files formatted in the same manner as 23andMe. Because of that, it should be pretty straightforward to create a new parser based on the one already written for 23andMe. If you are interested, I could test it out with some Genes for Good TXT files I have from a friend.

[yocontra]

@pvjones Yeah that would be cool, shoot me a PR and I'll merge that in. If it's the same format then we don't need a new parser, we can just make an alias.

Also have a ticket open for SAM/BAM files #6

[pvjones]

Cool. I'm testing it out right now. One potential problem is that Genes for Good allows users to download various file formats. Only one of them works on my machine. The other formats offer "imputed" data and are much, much longer, with file-sizes around 200 MB. When I try to run these, I exceed the V8 memory limit and Node crashes. You could prevent this by disallowing any of the longer imputed file types, by adding a condition in the return for 'matches' checking indexOf('unphased').

[yocontra]

published