SNPMStat_HM
Input
SNPMStat_HM reads in two data files genotype.txt and phase.txt, which can be directly downloaded from the International HapMap Project by browsing a genomic region in the GBrowse viewer on the project website and then using the SNP Genotype Data and Phased Haplotype Data Dumper plugin. Make sure you select fwd for Strand when you configure the data and name the data files genotype.txt and phase.txt accordingly when you download the data. They should be input as they are; the headers should be retained. There is an exception in downloading phased haplotype data for population group CHB or JPT in phase I & II database, as they are lumped together. Since the current version of SNPMStat_HM only allows one population at a time, extra manual work is needed to get rid of the unneeded one.
Output
SNPMStat_HM outputs two data files reference.dat and phase.dat, which can be directly used by SNPMStat.
Options
| Option | Default | Description | Example |
|---|---|---|---|
| -YRI | CEU | Specify the population as Yoruba in Ibadan, Nigeria | |
| -CHB | CEU | Specify the population as Han Chinese in Beijing, China | |
| -JPT | CEU | Specify the population as Japanese in Tokyo, Japan | |
| -np | No phased haplotype file available | |
Example
The example input and output data files can be found in the zipped package below and can be run by the command
Download
SNPMStat_HM for Windows [updated 09 December 2008]
SNPMStat_HM for Linux [updated 09 December 2008]
static binary executable (zip archive) » SNPMStat_HM_static.zip
Example files [updated 09 December 2008]
