Various scripts for SNP table convertion, modification and processing etc...
Perl
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LICENSE
README.md
SNP_HapMapFilterMissing.pl
SNP_HapMapToNumeric.pl

README.md

SNP Toolset

Various scripts for SNP table convertion, modification and processing etc...

SNP_HapMapToNumeric.pl - To convert your HapMap-type of SNP tables into numeric version. This is usefull for doing GWAS study if input is required to be numeric.

Usage:

perl SNP_HapMapToNumeric.pl snp-file start-column  

Example:

perl SNP_HapMapToNumeric.pl snp-table.hmp.txt 12  

Description: Program takes two argument, first argument is the HapMap file and second is the starting column number for the data (assuming first few columns are informative columns). If your data does not have any informative columns prior to SNP columns, enter 0 (zero). If it is HapMap data, you would like to use 12.

SNP_HapMapFilterMissing.pl - Filtering HapMap file based on the missing value.

Usage:

perl SNP_HapMapFilterMissing.pl snp-file cut-off  

Example:

perl SNP_HapMapFilterMissing.pl snp-table.hmp.txt 30  

Description: Program takes two argument, first argument is the HapMap file and second is the cut-off filter for the missing value.