[Biopython-dev] [GSoC] GSoC python variant update 6

Brad Chapman chapmanb at 50mail.com
Mon Jul 2 10:36:39 UTC 2012

Thanks for the updates and thoughts. I like the direction you're moving
after taking everything you've learned from the SQL experiments.

My general suggestions would be:

- Leverage PyVCF for all of the backend parsing. We want to remain
  compatible with this since merging/interfacing with the work James and
  everyone is doing is a primary goal. Keeping a similar code structure
  is a great way to facilitate this.

- For HGVS the general idea is to not be too tied to the VCF format, so
  I wouldn't worry about strict compatibility but rather use it to inform
  choices where you feel that things are mirroring VCF structure rather
  than more general variant representation.

> Another question that may reveal my complete ignorance of haplotypes
> and such: could a polyploid site ever be partially phased? e.g. a
> triploid genotype of 0/1|0?

It's possible but this is kind of a fringe case right now so I wouldn't
especially worry about it.

Thanks again,

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