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Multi tool use

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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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    What do you have so far? Where are you stuck?
    – glenn jackman
    1 hour ago










  • Are you aware of the Bioinformatics StackExchange site? They too are not a script writing service.
    – Kusalananda
    1 hour ago










  • You will need the split function and a for loop with an if / else if / else if statement in it.
    – glenn jackman
    1 hour ago










  • Gavin, please read unix.stackexchange.com/help/how-to-ask and come back to edit your question.
    – glenn jackman
    1 hour ago










  • I am thinking something: awk 'split ($4, myArray, ",") {if ($5 ~ "0/0") print $3 else if ($3 ~ "1/1") print $4 else if ($3 ~ "2/2") print ,$4 input_file
    – Gavin
    23 mins ago















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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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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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  • 1




    What do you have so far? Where are you stuck?
    – glenn jackman
    1 hour ago










  • Are you aware of the Bioinformatics StackExchange site? They too are not a script writing service.
    – Kusalananda
    1 hour ago










  • You will need the split function and a for loop with an if / else if / else if statement in it.
    – glenn jackman
    1 hour ago










  • Gavin, please read unix.stackexchange.com/help/how-to-ask and come back to edit your question.
    – glenn jackman
    1 hour ago










  • I am thinking something: awk 'split ($4, myArray, ",") {if ($5 ~ "0/0") print $3 else if ($3 ~ "1/1") print $4 else if ($3 ~ "2/2") print ,$4 input_file
    – Gavin
    23 mins ago













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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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CP001875.2 255 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
CP001875.2 324 C A,G 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 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 2/2 0/0 2/2 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 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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CP001875.2 372 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 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
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
CP001875.2 489 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 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 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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edited 4 mins ago





















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asked 1 hour ago









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  • 1




    What do you have so far? Where are you stuck?
    – glenn jackman
    1 hour ago










  • Are you aware of the Bioinformatics StackExchange site? They too are not a script writing service.
    – Kusalananda
    1 hour ago










  • You will need the split function and a for loop with an if / else if / else if statement in it.
    – glenn jackman
    1 hour ago










  • Gavin, please read unix.stackexchange.com/help/how-to-ask and come back to edit your question.
    – glenn jackman
    1 hour ago










  • I am thinking something: awk 'split ($4, myArray, ",") {if ($5 ~ "0/0") print $3 else if ($3 ~ "1/1") print $4 else if ($3 ~ "2/2") print ,$4 input_file
    – Gavin
    23 mins ago













  • 1




    What do you have so far? Where are you stuck?
    – glenn jackman
    1 hour ago










  • Are you aware of the Bioinformatics StackExchange site? They too are not a script writing service.
    – Kusalananda
    1 hour ago










  • You will need the split function and a for loop with an if / else if / else if statement in it.
    – glenn jackman
    1 hour ago










  • Gavin, please read unix.stackexchange.com/help/how-to-ask and come back to edit your question.
    – glenn jackman
    1 hour ago










  • I am thinking something: awk 'split ($4, myArray, ",") {if ($5 ~ "0/0") print $3 else if ($3 ~ "1/1") print $4 else if ($3 ~ "2/2") print ,$4 input_file
    – Gavin
    23 mins ago








1




1




What do you have so far? Where are you stuck?
– glenn jackman
1 hour ago




What do you have so far? Where are you stuck?
– glenn jackman
1 hour ago












Are you aware of the Bioinformatics StackExchange site? They too are not a script writing service.
– Kusalananda
1 hour ago




Are you aware of the Bioinformatics StackExchange site? They too are not a script writing service.
– Kusalananda
1 hour ago












You will need the split function and a for loop with an if / else if / else if statement in it.
– glenn jackman
1 hour ago




You will need the split function and a for loop with an if / else if / else if statement in it.
– glenn jackman
1 hour ago












Gavin, please read unix.stackexchange.com/help/how-to-ask and come back to edit your question.
– glenn jackman
1 hour ago




Gavin, please read unix.stackexchange.com/help/how-to-ask and come back to edit your question.
– glenn jackman
1 hour ago












I am thinking something: awk 'split ($4, myArray, ",") {if ($5 ~ "0/0") print $3 else if ($3 ~ "1/1") print $4 else if ($3 ~ "2/2") print ,$4 input_file
– Gavin
23 mins ago





I am thinking something: awk 'split ($4, myArray, ",") {if ($5 ~ "0/0") print $3 else if ($3 ~ "1/1") print $4 else if ($3 ~ "2/2") print ,$4 input_file
– Gavin
23 mins ago
















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