convert the numeric allele calls into nucleotide calls

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CHROM POS REF ALT PANS_1_1 PANS_1_10 PANS_1_2 PANS_1_5 PANS_1_6 PANS_1_8 PANS_1_9 PANS_200_1 PANS_200_2 PANS_2_1 PANS_2_5 PANS_2_6 PANS_2_7 PANS_2_8 PANS_4_2 PANS_99_11 PANS_99_22 PANS_99_23 PANS_99_24 PANS_99_25 PANS_99_26 PANS_99_27 PANS_99_29 PANS_99_31 PANS_99_32 PANS_99_33 PANS_99_36 PANS_99_4 PANS_99_5 PANS_99_9 PAN_02_2 PNA_02_12 PNA_03_1 PNA_03_2 PNA_03_3 PNA_05_1 PNA_06_1 PNA_06_4 PNA_07_1 PNA_07_10 PNA_07_13 PNA_07_14 PNA_07_22 PNA_07_5 PNA_07_7 PNA_08_1 PNA_11_1 PNA_13_1 PNA_14_2 PNA_15_1 PNA_15_2 PNA_15_3 PNA_18_1 PNA_18_10 PNA_18_10S PNA_18_2 PNA_18_3S PNA_18_5 PNA_18_5S PNA_18_6S PNA_18_7S PNA_18_8S PNA_18_9S PNA_200_1 PNA_200_10 PNA_200_11 PNA_200_12 PNA_200_13 PNA_200_3 PNA_200_5 PNA_200_7 PNA_200_8 PNA_92_7 PNA_97_11 PNA_97_2 PNA_97_3 PNA_97_8 PNA_98_1 PNA_98_11 PNA_98_12 PNA_98_2 PNA_98_3 PNA_98_7 PNA_98_8 PNA_99_1 PNA_99_14 PNA_99_2 PNA_99_3 PNA_99_6 PNA_99_7 PNA_99_8 PNA_99_9



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CP001875.2 904 G A 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0



Need to use awk to convert the allele calls in col 5 onwards
0/0 to the ref value in col 3
1/1 to the alt value in col 4
2/2 to the alt vlaue in col 4 after ,






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    CHROM POS REF ALT PANS_1_1 PANS_1_10 PANS_1_2 PANS_1_5 PANS_1_6 PANS_1_8 PANS_1_9 PANS_200_1 PANS_200_2 PANS_2_1 PANS_2_5 PANS_2_6 PANS_2_7 PANS_2_8 PANS_4_2 PANS_99_11 PANS_99_22 PANS_99_23 PANS_99_24 PANS_99_25 PANS_99_26 PANS_99_27 PANS_99_29 PANS_99_31 PANS_99_32 PANS_99_33 PANS_99_36 PANS_99_4 PANS_99_5 PANS_99_9 PAN_02_2 PNA_02_12 PNA_03_1 PNA_03_2 PNA_03_3 PNA_05_1 PNA_06_1 PNA_06_4 PNA_07_1 PNA_07_10 PNA_07_13 PNA_07_14 PNA_07_22 PNA_07_5 PNA_07_7 PNA_08_1 PNA_11_1 PNA_13_1 PNA_14_2 PNA_15_1 PNA_15_2 PNA_15_3 PNA_18_1 PNA_18_10 PNA_18_10S PNA_18_2 PNA_18_3S PNA_18_5 PNA_18_5S PNA_18_6S PNA_18_7S PNA_18_8S PNA_18_9S PNA_200_1 PNA_200_10 PNA_200_11 PNA_200_12 PNA_200_13 PNA_200_3 PNA_200_5 PNA_200_7 PNA_200_8 PNA_92_7 PNA_97_11 PNA_97_2 PNA_97_3 PNA_97_8 PNA_98_1 PNA_98_11 PNA_98_12 PNA_98_2 PNA_98_3 PNA_98_7 PNA_98_8 PNA_99_1 PNA_99_14 PNA_99_2 PNA_99_3 PNA_99_6 PNA_99_7 PNA_99_8 PNA_99_9



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    CP001875.2 904 G A 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0



    Need to use awk to convert the allele calls in col 5 onwards
    0/0 to the ref value in col 3
    1/1 to the alt value in col 4
    2/2 to the alt vlaue in col 4 after ,






    awk






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      CHROM POS REF ALT PANS_1_1 PANS_1_10 PANS_1_2 PANS_1_5 PANS_1_6 PANS_1_8 PANS_1_9 PANS_200_1 PANS_200_2 PANS_2_1 PANS_2_5 PANS_2_6 PANS_2_7 PANS_2_8 PANS_4_2 PANS_99_11 PANS_99_22 PANS_99_23 PANS_99_24 PANS_99_25 PANS_99_26 PANS_99_27 PANS_99_29 PANS_99_31 PANS_99_32 PANS_99_33 PANS_99_36 PANS_99_4 PANS_99_5 PANS_99_9 PAN_02_2 PNA_02_12 PNA_03_1 PNA_03_2 PNA_03_3 PNA_05_1 PNA_06_1 PNA_06_4 PNA_07_1 PNA_07_10 PNA_07_13 PNA_07_14 PNA_07_22 PNA_07_5 PNA_07_7 PNA_08_1 PNA_11_1 PNA_13_1 PNA_14_2 PNA_15_1 PNA_15_2 PNA_15_3 PNA_18_1 PNA_18_10 PNA_18_10S PNA_18_2 PNA_18_3S PNA_18_5 PNA_18_5S PNA_18_6S PNA_18_7S PNA_18_8S PNA_18_9S PNA_200_1 PNA_200_10 PNA_200_11 PNA_200_12 PNA_200_13 PNA_200_3 PNA_200_5 PNA_200_7 PNA_200_8 PNA_92_7 PNA_97_11 PNA_97_2 PNA_97_3 PNA_97_8 PNA_98_1 PNA_98_11 PNA_98_12 PNA_98_2 PNA_98_3 PNA_98_7 PNA_98_8 PNA_99_1 PNA_99_14 PNA_99_2 PNA_99_3 PNA_99_6 PNA_99_7 PNA_99_8 PNA_99_9



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      CP001875.2 904 G A 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0



      Need to use awk to convert the allele calls in col 5 onwards
      0/0 to the ref value in col 3
      1/1 to the alt value in col 4
      2/2 to the alt vlaue in col 4 after ,






      awk






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      CHROM POS REF ALT PANS_1_1 PANS_1_10 PANS_1_2 PANS_1_5 PANS_1_6 PANS_1_8 PANS_1_9 PANS_200_1 PANS_200_2 PANS_2_1 PANS_2_5 PANS_2_6 PANS_2_7 PANS_2_8 PANS_4_2 PANS_99_11 PANS_99_22 PANS_99_23 PANS_99_24 PANS_99_25 PANS_99_26 PANS_99_27 PANS_99_29 PANS_99_31 PANS_99_32 PANS_99_33 PANS_99_36 PANS_99_4 PANS_99_5 PANS_99_9 PAN_02_2 PNA_02_12 PNA_03_1 PNA_03_2 PNA_03_3 PNA_05_1 PNA_06_1 PNA_06_4 PNA_07_1 PNA_07_10 PNA_07_13 PNA_07_14 PNA_07_22 PNA_07_5 PNA_07_7 PNA_08_1 PNA_11_1 PNA_13_1 PNA_14_2 PNA_15_1 PNA_15_2 PNA_15_3 PNA_18_1 PNA_18_10 PNA_18_10S PNA_18_2 PNA_18_3S PNA_18_5 PNA_18_5S PNA_18_6S PNA_18_7S PNA_18_8S PNA_18_9S PNA_200_1 PNA_200_10 PNA_200_11 PNA_200_12 PNA_200_13 PNA_200_3 PNA_200_5 PNA_200_7 PNA_200_8 PNA_92_7 PNA_97_11 PNA_97_2 PNA_97_3 PNA_97_8 PNA_98_1 PNA_98_11 PNA_98_12 PNA_98_2 PNA_98_3 PNA_98_7 PNA_98_8 PNA_99_1 PNA_99_14 PNA_99_2 PNA_99_3 PNA_99_6 PNA_99_7 PNA_99_8 PNA_99_9



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      CP001875.2 228 T C 1/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 0/0 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 1/1 1/1 1/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/0 1/1 0/0 1/1 1/1 1/1 1/1 0/0 0/0 1/1 1/1 1/1 0/0 1/1 1/1 0/0 0/0 0/0 ./. 1/1 0/0 1/1 1/1 0/0 1/1 0/0 1/1 0/0 0/0 1/1 0/0 0/0 0/0 1/1
      CP001875.2 255 A C 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0
      CP001875.2 267 G A 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0
      CP001875.2 312 C T 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0
      CP001875.2 318 T C 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0
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      CP001875.2 336 T A 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0
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      CP001875.2 483 G A 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0
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      CP001875.2 699 A C 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0
      CP001875.2 904 G A 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0



      Need to use awk to convert the allele calls in col 5 onwards
      0/0 to the ref value in col 3
      1/1 to the alt value in col 4
      2/2 to the alt vlaue in col 4 after ,






      awk




      awk





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