Please help me parse a VCF file. I am pasting a real example.
Input:
1 1014143 rs786201005 C T . . RS=786201005;RSPOS=1014143;dbSNPBuildID=144;SSR=0;SAO=1;VP=0x050068000605000002110100;GENEINFO=ISG15:9636;WGT=1;VC=SNV;PM;PMC;NSN;REF;ASP;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.11:g.1014143C>T;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=1;CLNSRCID=147571.0003;CLNSIG=5;CLNDSDB=MedGen:OMIM:Orphanet;CLNDSDBID=C4015293:616126:ORPHA319563;CLNDBN=Immunodeficiency_38_with_basal_ganglia_calcification;CLNREVSTAT=no_criteria;CLNACC=RCV000162196.3
1 1014228 rs1921 G A,C . . RS=1921;RSPOS=1014228;dbSNPBuildID=36;SSR=0;SAO=0;VP=0x050328000a0517053f000100;GENEINFO=ISG15:9636;WGT=1;VC=SNV;PM;PMC;S3D;SLO;NSM;REF;ASP;VLD;G5A;G5;HD;GNO;KGPhase1;KGPhase3;CLNALLE=1;CLNHGVS=NC_000001.11:g.1014228G>A;CLNSRC=.;CLNORIGIN=1;CLNSRCID=.;CLNSIG=2;CLNDSDB=MedGen;CLNDSDBID=CN169374;CLNDBN=not_specified;CLNREVSTAT=single;CLNACC=RCV000455759.1;CAF=0.6611,0.3389,.;COMMON=1
1 1014316 rs672601345 C CG . . RS=672601345;RSPOS=1014319;dbSNPBuildID=142;SSR=0;SAO=1;VP=0x050068001205000002110200;GENEINFO=ISG15:9636;WGT=1;VC=DIV;PM;PMC;NSF;REF;ASP;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.11:g.1014319dupG;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=1;CLNSRCID=147571.0002;CLNSIG=5;CLNDSDB=MedGen:OMIM:Orphanet;CLNDSDBID=C4015293:616126:ORPHA319563;CLNDBN=Immunodeficiency_38_with_basal_ganglia_calcification;CLNREVSTAT=no_criteria;CLNACC=RCV000148989.5
1 1014359 rs672601312 G T . . RS=672601312;RSPOS=1014359;dbSNPBuildID=142;SSR=0;SAO=1;VP=0x050068000605000002110100;GENEINFO=ISG15:9636;WGT=1;VC=SNV;PM;PMC;NSN;REF;ASP;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.11:g.1014359G>T;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=1;CLNSRCID=147571.0001;CLNSIG=5;CLNDSDB=MedGen:OMIM:Orphanet;CLNDSDBID=C4015293:616126:ORPHA319563;CLNDBN=Immunodeficiency_38_with_basal_ganglia_calcification;CLNREVSTAT=no_criteria;CLNACC=RCV000148988.5
1 1020183 rs539283387 G C . . RS=539283387;RSPOS=1020183;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000a05040026000100;GENEINFO=AGRN:375790;WGT=1;VC=SNV;NSM;REF;ASP;VLD;KGPhase3;CLNALLE=1;CLNHGVS=NC_000001.11:g.1020183G>C;CLNSRC=.;CLNORIGIN=1;CLNSRCID=.;CLNSIG=3;CLNDSDB=MedGen;CLNDSDBID=CN169374;CLNDBN=not_specified;CLNREVSTAT=single;CLNACC=RCV000424799.1;CAF=0.9904,0.009585;COMMON=1
1 1020216 rs764659938 C G . . RS=764659938;RSPOS=1020216;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000000a05040002000100;GENEINFO=AGRN:375790;WGT=1;VC=SNV;NSM;REF;ASP;VLD;CLNALLE=1;CLNHGVS=NC_000001.11:g.1020216C>G;CLNSRC=.;CLNORIGIN=1;CLNSRCID=.;CLNSIG=0;CLNDSDB=MedGen;CLNDSDBID=CN221809;CLNDBN=cancer;CLNREVSTAT=single;CLNACC=RCV000422793.1
And I need an output:
1014143 rs786201005 C T CLNSIG=5 CLNDBN=Immunodeficiency_38_with_basal_ganglia_calcification
1014228 rs1921 G A,C CLNSIG=2 CLNDBN=not_specified
1014316 rs672601345 C CG CLNSIG=5 CLNDBN=Immunodeficiency_38_with_basal_ganglia_calcification
1014359 rs672601312 G T CLNSIG=5 CLNDBN=Immunodeficiency_38_with_basal_ganglia_calcification
1020183 rs539283387 G C CLNSIG=3 CLNDBN=not_specified
1020216 rs764659938 C G CLNSIG=0 CLNDBN=not_provided
That means print column 2,3,4,5 and then parse last column and print just CLNSIG and CLNDBN. Problem is, that those values are not always in the same position.
My try was:
awk -v OFS="\t"'{print $2,$3,$4,$5,$8}' input
...and then I have no clue how to get CLNSIG and CLNDBN.
Thank you for any ideas.
With perl
$ perl -lane 'print join "\t",(@F[1..4], /(?:CLNSIG|CLNDBN)=[^;]+/g)' ip.txt
1014143 rs786201005 C T CLNSIG=5 CLNDBN=Immunodeficiency_38_with_basal_ganglia_calcification
1014228 rs1921 G A,C CLNSIG=2 CLNDBN=not_specified
1014316 rs672601345 C CG CLNSIG=5 CLNDBN=Immunodeficiency_38_with_basal_ganglia_calcification
1014359 rs672601312 G T CLNSIG=5 CLNDBN=Immunodeficiency_38_with_basal_ganglia_calcification
1020183 rs539283387 G C CLNSIG=3 CLNDBN=not_specified
1020216 rs764659938 C G CLNSIG=0 CLNDBN=cancer
-a option to split input on white-space, saved in @F array/(?:CLNSIG|CLNDBN)=[^;]+/g will return the CLNSIG and CLNDBN fields@F[1..4] gives fields 2nd to 5th (index starts from 0)-lane options