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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 303008268 by cmccabe on Wednesday 29th of November 2017 12:15:30 PM
Old 11-29-2017
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

desired output
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	.

other format of lines to skip
Code:
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

If I split on $8 using DP= and print the value up to the ;, since that tag is iin both lines, wont it print for both? However since $16 has a value in it that line can be skipped (the much larger of the two lines).

awk
Code:
awk -F'\t' -v OFS="\t" '{if (!$16);{split($8,a,[=;]); {print $1, $2, $3, $4, $5, $6, $7, $8, $9, $10, ".", ".", ".", ".", ".", a[1], "homref", "."}' file


Not sure is the above is any closer and I did not really know what would print, but understand better know? Thank you Smilie.

I also tried the perl below which executes but does not print any new output the desired output, but seems close.

perl
Code:
perl -plae ' 
 BEGIN{ %h = qw(0/0 homref) } /^[^#].*DP=(\d+);.*([0-0]\/[0-0])/ and $_ .= join "\t", ("", "."),".",".",".", ".", $1, $h{$7},"."' file > out

output of line to change --- seems to extract 224 and doesn't print homref though qw=0/0)
Code:
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	.	.	.	.	.	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  --- this line is correct ----

Last edited by cmccabe; 11-29-2017 at 03:08 PM.. Reason: fixed format and added perl
 

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