The DP= is in each line of the input file, however it is always at the start of $8 in the lines that the awk is goiog to update. $11 will also always be empty (like in line1, in line2 there is a value so nothing is done). All lines are printed that are in the input file, that is the comments and each line is printed. In the example since line2 is good it is only printed as is, but line1 needs to be updated brfore it is printed. Do the comment lines need to be skipped as they do not have more then twwo fields in them? Thank you .
file 11 tab-delimeted fields --- the actual file is over 22 million lines in the below format ----
line1 and all lines like it are the one that the awk updates
line2 and all lines like it are skipped(nothing needs to be done to them)
file
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
awk
Code:
awk ' # Run awk to process the following awk script...
BEGIN { OFS = "\t" } # Set output field separator.
'NR==FNR {if (!$11) { # For each line in the input file check if $11 is empty
split($8,a,"/[=;]/"); # if $11 is empty then split $8 on the = and ; and store the value in a
next # process next line in file
} # close block
{ # start print block
print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,".",".",".",".",".",a[2],"homref","."; # print desired output
} # close print block
next # print next line
}1' file # define input
I have syntax errors in the awk but added comments that I hope will help. I use one-liners cause for whatever reason I have a hard time not using them (as evident by the syntax errors).... never-the-less commented seems to help. Thank you .
Last edited by cmccabe; 11-29-2017 at 07:34 PM..
Reason: fixed format
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