Shell Programming and Scripting

2    168611167    STK39    STK39    ---    27347    "serine threonine kinase 39 (STE20/SPS1 homolog, yeast)"    YES    SNP_A-2086192    rs16854601    0.001558882
6    13670256    SIRT5 /// RPS4X    SIRT5    ---    23408 /// 6191    "sirtuin (silent mating type information regulation 2 homolog) 5 (S. cerevisiae) /// ribosomal protein S4, X-linked"    YES    SNP_A-8405097    rs16874223    0.00156082
2    105439878    NCK2 /// FHL2    FHL2 /// NCK2    ---    8440 /// 2274    NCK adaptor protein 2 /// four and a half LIM domains 2    ---    SNP_A-2034891    rs41322544    0.001562043
12    80373503    PPFIA2    PPFIA2    ---    8499    "protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 2"    YES    SNP_A-8542673    rs17008588    0.001565901
15    41547066    TP53BP1 /// TP53BP1 /// TP53BP1    TP53BP1    ---    7158 /// 7158 /// 7158    tumor protein p53 binding protein 1 /// tumor protein p53 binding protein 1 /// tumor protein p53 binding protein 1    YES    SNP_A-1782700    rs1814538    0.001573326

parse.awk

{
    for(i=1;i<NF;i++){
        if ($i ~ /^SNP_A/){
            a_str[NR]=sprintf("%s %s",$i,$(i+1))
            a_val[NR]=$NF
            break
        }
}
}
END{
    for(i in a_str) print a_str[i],a_val[i]
}

$ awk -f parse.awk yourFile | sort -k3,3

{
    for(i=1;i<NF;i++){
        if ($i ~ /^SNP_A/){
            a_str[$NF]=sprintf("%s %s",$i,$(i+1))
            break
        }
}
}
END{
    n=asorti(a_str, a_copy)
    for(i=1; i<=n; i++) print a_str[a_copy[i]]
}