An Efficient Tagger Program For Genome Scale Data

Question

[sci11168]

Hi there:

Just wonder if there is any user friendly tagging SNP generator that can handle genome scale data easily?

The reason is that I have a list of SNP from all over the genome and want to see how efficient they can tag other common SNPs. Therefore it would be nice for the tagger to have the features below:

1. Handle all SNPs on a single chromosome
2. Capable to download raw data from HapMap with customized MAF cutoff
3. Force including the list of SNPs I have.

I've tried HaploView which seems to be great for requirement 2 and 3 but it throws error for requirement 1.

Thanks for your kind help.

Answer 1

[sci11168]

OK. Think Tagger in Haploview should be the answer and the initial problem encountered is due to not enough RAM assigned.

Tagger seems to require 6G RAM for big chromosomes like Chr1 and it peacefully terminates once such requirement is fulfilled.