The limits of computational power – shades of 1982

By Razib Khan | March 29, 2011 1:44 pm

Two Steps Forward, Two Steps Back:

I got my daughter a netbook, so now my computer is doing Harappa Prohect work 24×7.

Also, Simranjit was nice enough to offer me the use of a server. For privacy reasons, I am not going to upload any of the participants’ data there but it is much faster than my machine and hence very useful for running Admixture on the reference data (especially with crossvalidation).

As for steps back, I downloaded the current 1000genomes data (1,212 samples, 2.4 million SNPs). It’s in vcf format. Using vcftools to convert it to ped format will take about 3 weeks. Yes you heard that right. BTW, the good stuff from a South Asian point of view will come later this year with a 100 Assamese AhomF, 100 Kayadtha from Calcutta, 100 Reddys from Hyderabad, 100 Maratha from Bombay and 100 Lahori Punjabis.

Also, I spent most of Sunday evening and night in the ER and got a diagnosis of ureterolithiasis for my efforts. All I can say is: Three cheers for Percocet!!

First, wish Zack well. Second, he has over 70 individuals in the Harappa Ancestry Project data base (in addition to the public data sets). If you’re South Asian, Iranian, Burmese, or Tibetan, here are the details of participation.

CATEGORIZED UNDER: Genetics, Genomics
  • http://dienekes.blogspot.com Dienekes

    I’ll be happy to share my C++ code with any genome bloggers/scientists who ask at dodecad@gmail.com (I’ve already sent it to Zack). I shudder to think how vcftools was written to be so damn slow.

  • Sandgroper

    *embittered humorless laughter*

    Yeah, I got my daughter a netbook.

    Now she has two laptops, one Apple and one Microsoft-compatible “just in case”, and an iPad, and I’m using the !@#$%^ netbook. Going through airport security she’s a total embarrassment.

    Watch out for smart daughers, Zack, they take over. Today 6 years old, tomorrow ze world. The upside is they love and care about their dumb old fathers.

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Gene Expression

This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!

About Razib Khan

I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. In relation to nationality I'm a American Northwesterner, in politics I'm a reactionary, and as for religion I have none (I'm an atheist). If you want to know more, see the links at http://www.razib.com

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