January 16, 2012

Phased Omni haplotypes with ShapeIT

The working directory of the 1000 Genomes ftp site contains phased haplotypes for 2,123 individuals from the 1000 Genomes Project (US/Europe). The data were phased with ShapeIT, which I've recently played with, and could recommend as a fairly user-friendly and high quality phasing software.

You can use vcftools to convert the data into PLINK format, which appears to be quite efficient (but use --plink-tped) compared to doing it on the single file I previously linked to. So, it's also a way to get 1000Genomes data into the more useful PLINK format, and it's pre-phased as a bonus.

2 comments:

bau said...

Can Plink manage phased data? How?
Thank you!
Francesco

Faye said...

Both Napoleon Bonaparte and Adolph Hitler were Zionist Jew bastards, whose forefathers were the Rothschilds. Eb1b1 is the DNA of Solomon Meyer Rothschild of Austria, who turns out to be Hitler's grandfather. Hitler's grandmother was Solomon's maid and Solomon fostered a Jew bastard named Aloi Hitler, who is Hitler's father. Obviously, the Zionist Jews fomented the French Revolution and World War I + II to depose the French Emperor and German Emperor and replaced it not with democracy, but rather with their own blood-line.