*Usage:

  ./blimp -p panel_file -m map_file -r rmb_file -d input_freq [ -t target_list -o output_file ] [ -unphased ]

*Required input files:

1. panel_file: an nxp matrix of genotypes, where n is the number of individuals and p is the number of SNPs, e.g. The hapmap phased data file can be directly used here.

2. map_file:  this file denotes the all p SNPs appeared in panel_file, it follows hapmap legend file format.

3. rmb_file: lists recombination rate between all adjacent markers in the panel. This file can be converted from recombination rate file in IMPUTE format and corresponding map_file by running the following perl script (included in the package):
     
      perl make_r.pl map_file impute_genetic_map haplotype_size  > rmb_file

for Hapmap ceu panel haplotype_size is 120 

4. input_freq: this file denotes the subset of SNPs whose allele frequencies are observed. Each line of the input file is formated as follows

       rs#  allele_frequency

*Optional input files:

1. target_list: a list of untyped SNPs whose allele frequencies are to be imputed. This file simply lists markers of interest in lines. If this file is not provided, all untyped SNPs from map_file will be imputed.

2. output_file: the name of user specified output file. If it is unspecified, the output will be directed to standard out (i.e. screen). 


*Other option:
 
If the panel is un-phased, use option "-unphased". 


*Important issue:

The strand issue must be taken care of, before running the program, i.e. the frequencies listed in input file must match the panel annotation of 0 and 1. 


*Output format

The output format is as follows

  rs#   estimated_allele_frequency  standard_error