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Full Discussion: awk to add value and text to specific lines
Top Forums Shell Programming and Scripting awk to add value and text to specific lines Post 303008287 by Don Cragun on Wednesday 29th of November 2017 10:29:24 PM
Old 11-29-2017
Assuming that your sample data is representative, the following seems to do what you want:
Code:
awk '
BEGIN {	FS = OFS = "\t"
}
NF == 10 {
	split($8, a, /[=;]/)
	$11 = $12 = $13 = $14 = $15 = $18 = "."
	$16 = (a[1] == "DP") ? a[2] : "DP=num_Missing"
	$17 = "homref"
}
1' file

Note that this assumes that lines that are to be modified only have 10 fields (i.e., 9 <tab>s) as in your sample. It verifies that field #8 does start with DP= and assigns a diagnostic message to field #16 if it isn't. This seemed safer to me than blindly assuming that the input file is correctly formatted. (And, I added a line to my sample input file to be sure that it worked as I expected. It didn't the first two times I tried it.)

When the contents of file is:
Code:
##bcftools_normVersion=1.3.1+htslib-1.3.1
##bcftools_normCommand=norm -m-both -o genome_split.vcf genome.vcf.gz
##bcftools_normCommand=norm -f /home/cmccabe/Desktop/NGS/picard-tools-1.140/resources/ucsc.hg19.fasta -o genome_annovar.vcf genome_split.vcf
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT
chr1	948797	.	C	.	0	PASS	DP=159;END=948845;MAX_DP=224;MIN_DP=95	GT:DP:MIN_DP:MAX_DP	0/0:159:95:224
chr1	948846	.	T	TA	1185.38	PASS	AF=0.986111;AO=200;DP=227;FAO=213;FDP=216;FDVR=0;FR=.;FRO=3;FSAF=132;FSAR=81;FSRF=3;FSRR=0;FWDB=-0.038073;FXX=0.0226234;HRUN=1;LEN=1;MLLD=24.748;OALT=A;OID=.;OMAPALT=TA;OPOS=948847;OREF=-;PB=.;PBP=.;QD=21.9515;RBI=0.0905281;REFB=0.0706997;REVB=0.0821327;RO=17;SAF=122;SAR=78;SRF=15;SRR=2;SSEN=0;SSEP=0;SSSB=-0.0430195;STB=0.505617;STBP=0.201;TYPE=ins;VARB=0.000148797	GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR	1/1:219:227:216:17:3:200:213:0.986111:78:122:15:2:81:132:3:0	0.986	132	81	1	GOOD	216	homalt	36
ALT1	948798	.	D	.	1	PAST	END=948845;MAX_DP=224;MIN_DP=95;DP=159	GT:DP:MIN_DP:MAX_DP	1/1:160:96:225

then the output produced is:
Code:
##bcftools_normVersion=1.3.1+htslib-1.3.1
##bcftools_normCommand=norm -m-both -o genome_split.vcf genome.vcf.gz
##bcftools_normCommand=norm -f /home/cmccabe/Desktop/NGS/picard-tools-1.140/resources/ucsc.hg19.fasta -o genome_annovar.vcf genome_split.vcf
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT
chr1	948797	.	C	.	0	PASS	DP=159;END=948845;MAX_DP=224;MIN_DP=95	GT:DP:MIN_DP:MAX_DP	0/0:159:95:224	.	.	.	159	homref	.
chr1	948846	.	T	TA	1185.38	PASS	AF=0.986111;AO=200;DP=227;FAO=213;FDP=216;FDVR=0;FR=.;FRO=3;FSAF=132;FSAR=81;FSRF=3;FSRR=0;FWDB=-0.038073;FXX=0.0226234;HRUN=1;LEN=1;MLLD=24.748;OALT=A;OID=.;OMAPALT=TA;OPOS=948847;OREF=-;PB=.;PBP=.;QD=21.9515;RBI=0.0905281;REFB=0.0706997;REVB=0.0821327;RO=17;SAF=122;SAR=78;SRF=15;SRR=2;SSEN=0;SSEP=0;SSSB=-0.0430195;STB=0.505617;STBP=0.201;TYPE=ins;VARB=0.000148797	GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR	1/1:219:227:216:17:3:200:213:0.986111:78:122:15:2:81:132:3:0	0.986	132	81	1	GOOD	216	homalt	36
ALT1	948798	.	D	.	1	PAST	END=948845;MAX_DP=224;MIN_DP=95;DP=159	GT:DP:MIN_DP:MAX_DP	1/1:160:96:225	.	.	.	DP=num_Missing	homref	.

Hopefully, this will come close to what you want.
This User Gave Thanks to Don Cragun For This Post:
cmccabe
 

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