PyCon 2015 talk notes for "How to interpret your own genome"

Here are talk notes and links for my PyCon 2015 talk.

The talk slides are up on SlideShare.


General background

You should definitely check out Mike Lin's great blog posts on "Blogging my genome".

I found SNPedia through this wonderful blog post on how to use 23andMe irresponsibly, on Slate Star Codex.

My introduction to bcbio came from Brad Chapman's excellent blog post on evaluating and comparing variant detection methods.

There are several openly available benchmarking data sets for human genetics/genomics. The Ashkenazim data set I used for my talk is here, and you can see the Personal Genome Project profile for the son, here. The raw data is available here, and you can see the resequencing report for the son, here.

The Personal Genome Project is something worth checking out.

More and more of human genetics and genomics is "open" -- check out the Variant Call Format (VCF) spec, now on github.


Pipeline

To run the bcbio variant calling pipeline I discuss in the talk, or examine the SNPs in the Ashkenazim trio with Gemini, take a look at my pipeline notes. The Gemini part will let you examine SNPs for the three individuals in the Ashkenazi trio, starting from the VCF files.

Slide notes

Slide 4: this link explains recombination and inheritance REALLY well.

This John Hawks' blog post is my source for 300-600 novel mutations per generation.

Slide 19:

You can read more about the Ashkenazi Jews here.

The data sets are available here.

Slide 27: Canavan Disease

Slides 30 and 31 from Demographic events and evolutionary forces shaping European genetic diversity by Veeramah and Novembre, 2014.

Slide 32 from Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls, 2007.

Slide 35: the "narcissome" link

Slide 36: a paper on lack of concordance amongst variant callers.

Slide 37: the gene drive link.

How to get involved

I asked the bcbio and gemini folk if there were any opportunities for Python folk to get involved in their work.

Here are some of their thoughts:

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