songtaogui / chip2hmp

small script that convert chip genotype.xls to hmp format

INSTALLATION

1. make sure csvtk is correctly installed and could be accessed in $PATH
2. clone the git repos, run bash wlab_chip2hmp.sh [options], or
3. make the script executable and add it to $PATH, so you could exec it anywhere through wlab_chip2hmp.sh

USAGE

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Convert Chip data to hmp format
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Dependence: csvtk, perl
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USAGE:
    bash wlab_chip2hmp.sh [Genotype.xls] [mode] [outputfile]
Opt:
    - [Genotype.xls]: Genotype format of chip, with columns of
        ID,chrom,position,ref,genotype(sample1),ref_depth(sample1)...
    - [mode]: seq or num.
        if seq, geno would be "AA,TT,CC,GG", and "NN" for missing;
        if num, geno would be number of alt alleles, "0,1,2", and "-9" for missing;

** NOTE: Only output biallele SNP sites;
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Author: Songtao Gui
E-mail: [e-mail]