Wednesday, April 18, 2007

Perl scripts & LaTeX

Not really related to any news, but I've written a couple of perl scripts for formatting the output from two tagging programs. In both cases the scripts take the standard output and generate LaTeX formatted tables for subsequent use.

Tagger (de Bakker et al 2005) is implemented in the program Haploview, and uses pair-wise LD to tag regions. The script for re-formatting the output is written in perl and is available here.

ldSelect (Carlson et al 2004) is an alternative method of tagging SNPs, but also based on LD. The output format from this is (in my opinion) a little awkward as the output uses the base-pair positions (mainly because the input file format is Prettybase). Thus in addition to the output file this script requires the user to provide a tab-delimited text file of the markers and their base-pair positions and will convert the base-pair positions of markers to their rs numbers in the resulting latex table. The script is again written in perl and is available here.


Carlson, C. S., Eberle, M. A., Rieder, M. J., Yi, Q., Kruglyak, L., Nickerson, D. A. (2004) Selecting a maximally informative set of single- nucleotide polymorphisms for association analyses using linkage disequilibrium American Journal of Human Genetics 74:106-120 PDF on PubMed

de Bakker, P. I. Yelensky, R. Pe'er, I. Gabriel, S. B. Daly, M. J., Altshuler, D. (2005) Efficiency and power in genetic association studies. Nature Genetics 37:1217-1223