Quote:
chr1 412573 . A C 2758.77 . AC=2;AF=1.00;AN=2;DP=71;Dels=0.00;FS=0.000;HaplotypeScore=2.8822;MLEAC=2;MLEAF=1.00;MQ=58.36;MQ0=0;Q D=38.86;resource.EFF=INTERGENIC(MODIFIER||||||||) GT:AD
P:GQ:PL 1/1:0,71:71:99:2787,214,0 GATKSAM
chr1 602567 rs21953190 A G 5481.77 . AC=2;AF=1.00;AN=2;DB;DP=152;Dels=0.00;FS=0.000;HaplotypeScore=6.8385;MLEAC=2;MLEAF=1.00;MQ=59.09;MQ0 =0;QD=36.06;resource.EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D1034|ADNP2|protein_coding|CODING|ENSCAFT00000000008|5) GT:AD
P:GQ:PL 1/1:0,151:151:99:5510,430,0 GATKSAM
I have text file with lines as shown here. Each row has 11 columns separated by tab. In each row, i want to split the 8th column such that the output should look like shown below. Here value in the 9th column is DP value and in the 10th column is MQ value followed by the values after resource.EFF=.
chr1 412573 . A C 2758.77 . 71 58.36 INTERGENIC MODIFIER GT:AD
P:GQ:PL 1/1:0,71:71:99:2787,214,0 GATKSAM
chr1 602567 rs21953190 A G 5481.77 . 152 59.09 SYNONYMOUS_CODING LOW SILENT gaT/gaC D1034 ADNP2 protein_coding CODING ENSCAFT00000000008 5 GT:AD
P:GQ:PL 1/1:0,151:151:99:5510,430,0 GATKSAM
Which means the 8th column has to be cleaned up such that, it has only DP value, MQ value and the information after resource.EFF= separated by tabs.
Could anyone help?