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Full Discussion: awk colon separated items
Top Forums UNIX for Dummies Questions & Answers awk colon separated items Post 302968824 by RavinderSingh13 on Tuesday 15th of March 2016 01:18:16 AM
Old 03-15-2016
Hello janshamsani,

Let's say following is your Input_file(I have taken data from your Input_file only as there was no line having value more than .25 so add one more line to it as follows.).
Code:
1       11291088        T       TA      1       TCGA-AP-A0LH_W_IlluminaGA-DNASeq_exome  15      PASS    1       INS     1011    ZERO    frameshift_variant      MTOR   HIGH     tta/ttTa        CODING  protein_coding  ENST00000361445 GT:DP:AD:BQ:MQ:SB:FA:SS:SSC:MQA NORMAL=<0/1:507:500,7:.:.:.:0.014:0:15:.>       PRIMARY=<0/1:504:499,5:.:.:.:0.01:1:15:.>
1       16255141        GGA     G       91      TCGA-AX-A0IW_W_IlluminaGA-DNASeq_exome  15      PASS    1       DEL     638     ZERO    frameshift_variant      SPEN   HIGH     gag/    CODING  protein_coding  ENST00000375759 GT:DP:AD:BQ:MQ:SB:FA:SS:SSC:MQA NORMAL=<0/1:266:261,5:.:.:.:0.019:0:15:.>       PRIMARY=<0/1:372:367,5:.:.:.:0.013:1:15:.>
1       16255169        G       GA      1       TCGA-AP-A0LH_W_IlluminaGA-DNASeq_exome  15      PASS    1       INS     1020    ZERO    frameshift_variant      SPEN   HIGH     gaa/gAaa        CODING  protein_coding  ENST00000375759 GT:DP:AD:BQ:MQ:SB:FA:SS:SSC:MQA NORMAL=<0/1:510:499,11:.:.:.:0.022:0:15:.>      PRIMARY=<0/1:510:500,10:.:.:.:0.02:1:15:.>
1       16255186        C       CA      1       TCGA-AP-A0LH_W_IlluminaGA-DNASeq_exome  15      PASS    1       INS     1018    ZERO    frameshift_variant      SPEN   HIGH     aaa/Aaaa        CODING  protein_coding  ENST00000375759 GT:DP:AD:BQ:MQ:SB:FA:SS:SSC:MQA NORMAL=<0/1:509:498,11:.:.:.:0.022:0:15:.>      PRIMARY=<0/1:509:500,9:.:.:.:0.018:1:15:.>
1       16255424        G       GA      1       TCGA-AP-A0LH_W_IlluminaGA-DNASeq_exome  15      PASS    1       INS     1012    ZERO    frameshift_variant      SPEN   HIGH     gaa/gAaa        CODING  protein_coding  ENST00000375759 GT:DP:AD:BQ:MQ:SB:FA:SS:SSC:MQA NORMAL=<0/1:507:500,7:.:.:.:0.014:0:15:.>       PRIMARY=<0/1:505:499,6:.:.:.:0.012:1:15:.>
1       16255559        G       GA      1       TCGA-AP-A0LH_W_IlluminaGA-DNASeq_exome  15      PASS    1       INS     1010    ZERO    frameshift_variant      SPEN   HIGH     gaa/gAaa        CODING  protein_coding  ENST00000375759 GT:DP:AD:BQ:MQ:SB:FA:SS:SSC:MQA NORMAL=<0/1:504:499,5:.:.:.:0.01:0:15:.>        PRIMARY=<0/1:506:500,6:.:.:.:0.012:1:15:.>
1       16255727        C       CA      1       TCGA-AP-A0LH_W_IlluminaGA-DNASeq_exome  15      PASS    1       INS     684     ZERO    frameshift_variant      SPEN   HIGH     caa/cAaa        CODING  protein_coding  ENST00000375759 GT:DP:AD:BQ:MQ:SB:FA:SS:SSC:MQA NORMAL=<0/1:387:381,6:.:.:.:0.016:0:15:.>       PRIMARY=<0/1:297:292,5:.:.:.:0.017:1:15:.>
1       16255727        C       CA      1       TCGA-AP-A0LH_W_IlluminaGA-DNASeq_exome  15      PASS    1       INS     684     ZERO    frameshift_variant      SPEN    HIGH    caa/cAaa        CODING  protein_coding  ENST00000375759 GT:DP:AD:BQ:MQ:SB:FA:SS:SSC:MQA NORMAL=<0/1:387:381,6:.:.:.:0.016:0:15:.>       PRIMARY=<0/1:297:292,5:.:.:.:0.27:1:15:.>

Now following code may help you in same.
Code:
awk '{split($NF, array,":");if(array[7]>0.25){print $0}}'  Input_file

Output will be as follows then.
Code:
1       16255727        C       CA      1       TCGA-AP-A0LH_W_IlluminaGA-DNASeq_exome  15      PASS    1       INS     684     ZERO    frameshift_variant      SPEN    HIGH    caa/cAaa        CODING  protein_coding  ENST00000375759 GT:DP:AD:BQ:MQ:SB:FA:SS:SSC:MQA NORMAL=<0/1:387:381,6:.:.:.:0.016:0:15:.>       PRIMARY=<0/1:297:292,5:.:.:.:0.27:1:15:.>

Hope this helps you. Let me know if you have any queries on same.


Thanks,
R. Singh
This User Gave Thanks to RavinderSingh13 For This Post:
janshamsani
 

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