The awk below executes and produces the current output, which is correct, except I can not seem to include the header lines # and ## in the output as well. I tried adding !/^#/ thinking that it would skip the lines with # and output them but the entire file prints as is. Thank you .
file
Code:
##bcftools_normVersion=1.9+htslib-1.9
##bcftools_normCommand=norm --do-not-normalize -m -both /path/to/xxxxx.vcf; Date=Tue Feb 26 12:59:30 2019
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT xxxx
chr1 11174372 MTOR A <CNV> 100 PASS FR=.;PRECISE=FALSE;SVTYPE=CNV;END=11217311;LEN=42939;NUMTILES=7;SD=0.47;CDF_MAPD=0.01:1.480581,0.025:1.544948,0.05:1.602554,0.1:1.671659,0.2:1.759366,0.25:1.793881,0.5:1.94,0.75:2.098021,0.8:2.139179,0.9:2.251416,0.95:2.348502,0.975:2.436069,0.99:2.541976;REF_CN=2;CI=0.05:1.60255,0.95:2.3485;RAW_CN=1.94;FUNC=[{'gene':'MTOR'}] GT:GQ:CN ./.:0:1.94
chr1 11174383 COSM1161896 A G 264.674 PASS AF=0;AO=0;DP=4229;FAO=0;FDP=2000;FDVR=5;FR=.;FRO=2000;FSAF=0;FSAR=0;FSRF=1166;FSRR=834;FWDB=-0.0180893;FXX=0;HRUN=1;HS_ONLY=0;LEN=1;MLLD=127.881;OALT=G;OID=COSM1161896;OMAPALT=G;OPOS=11174383;OREF=A;PB=.;PBP=.;QD=0.529347;RBI=0.0955223;REFB=9.08841e-06;REVB=0.0937938;RO=4212;SAF=0;SAR=0;SRF=2442;SRR=1770;SSEN=0;SSEP=0;SSSB=3.6281e-08;STB=0.5;STBP=1;TYPE=snp;VARB=0;HS;FUNC=[{'transcript':'NM_004958.3','gene':'MTOR','location':'exonic','exon':'53'}] GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR 0/0:264:4229:2000:4212:2000:0:0:0:0:0:2442:1770:0:0:1166:834
chr1 43814978 COSM1342796;COSM86963 A G 231.262 PASS AF=0.0010005;AO=4;DP=3351;FAO=2;FDP=1999;FDVR=10;FR=.,.;FRO=1997;FSAF=1;FSAR=1;FSRF=944;FSRR=1053;FWDB=0.00987233;FXX=0.000499998;HRUN=1;HS_ONLY=0;LEN=1,1;MLLD=106.81;OALT=G,T;OID=COSM1342796,COSM86963;OMAPALT=G,T;OPOS=43814978,43814978;OREF=A,A;PB=.;PBP=.;QD=0.462755;RBI=0.014386;REFB=4.80559e-05;REVB=0.010464;RO=3338;SAF=1;SAR=3;SRF=1576;SRR=1762;SSEN=0;SSEP=0;SSSB=-0.0113679;STB=0.526994;STBP=0.848;TYPE=snp;VARB=-0.0370454;HS;FUNC=[{'transcript':'NM_005373.2','gene':'MPL','location':'exonic','exon':'10'}] GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR 0/0:231:3351:1999:3338:1997:4:2:0.0010005:3:1:1576:1762:1:1:944:1053
chr1 43814978 COSM1342796;COSM86963 A G 231.262 PASS AF=0.05;AO=4;DP=3351;FAO=2;FDP=1999;FDVR=10;FR=.,.;FRO=1997;FSAF=1;FSAR=1;FSRF=944;FSRR=1053;FWDB=0.00987233;FXX=0.000499998;HRUN=1;HS_ONLY=0;LEN=1,1;MLLD=106.81;OALT=G,T;OID=COSM1342796,COSM86963;OMAPALT=G,T;OPOS=43814978,43814978;OREF=A,A;PB=.;PBP=.;QD=0.462755;RBI=0.014386;REFB=4.80559e-05;REVB=0.010464;RO=3338;SAF=1;SAR=3;SRF=1576;SRR=1762;SSEN=0;SSEP=0;SSSB=-0.0113679;STB=0.526994;STBP=0.848;TYPE=snp;VARB=-0.0370454;HS;FUNC=[{'transcript':'NM_005373.2','gene':'MPL','location':'exonic','exon':'10'}] GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR 0/0:231:3351:1999:3338:1997:4:2:0.0010005:3:1:1576:1762:1:1:944:1053
current output
Code:
chr1 43814978 COSM1342796;COSM86963 A G 231.262 PASS AF=0.05;AO=4;DP=3351;FAO=2;FDP=1999;FDVR=10;FR=.,.;FRO=1997;FSAF=1;FSAR=1;FSRF=944;FSRR=1053;FWDB=0.00987233;FXX=0.000499998;HRUN=1;HS_ONLY=0;LEN=1,1;MLLD=106.81;OALT=G,T;OID=COSM1342796,COSM86963;OMAPALT=G,T;OPOS=43814978,43814978;OREF=A,A;PB=.;PBP=.;QD=0.462755;RBI=0.014386;REFB=4.80559e-05;REVB=0.010464;RO=3338;SAF=1;SAR=3;SRF=1576;SRR=1762;SSEN=0;SSEP=0;SSSB=-0.0113679;STB=0.526994;STBP=0.848;TYPE=snp;VARB=-0.0370454;HS;FUNC=[{'transcript':'NM_005373.2','gene':'MPL','location':'exonic','exon':'10'}] GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR 0/0:231:3351:1999:3338:1997:4:2:0.0010005:3:1:1576:1762:1:1:944:1053
desired output
Code:
##bcftools_normVersion=1.9+htslib-1.9
##bcftools_normCommand=norm --do-not-normalize -m -both /path/to/xxxxx.vcf; Date=Tue Feb 26 12:59:30 2019
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT xxxx
chr1 43814978 COSM1342796;COSM86963 A G 231.262 PASS AF=0.05;AO=4;DP=3351;FAO=2;FDP=1999;FDVR=10;FR=.,.;FRO=1997;FSAF=1;FSAR=1;FSRF=944;FSRR=1053;FWDB=0.00987233;FXX=0.000499998;HRUN=1;HS_ONLY=0;LEN=1,1;MLLD=106.81;OALT=G,T;OID=COSM1342796,COSM86963;OMAPALT=G,T;OPOS=43814978,43814978;OREF=A,A;PB=.;PBP=.;QD=0.462755;RBI=0.014386;REFB=4.80559e-05;REVB=0.010464;RO=3338;SAF=1;SAR=3;SRF=1576;SRR=1762;SSEN=0;SSEP=0;SSSB=-0.0113679;STB=0.526994;STBP=0.848;TYPE=snp;VARB=-0.0370454;HS;FUNC=[{'transcript':'NM_005373.2','gene':'MPL','location':'exonic','exon':'10'}] GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR 0/0:231:3351:1999:3338:1997:4:2:0.0010005:3:1:1576:1762:1:1:944:1053
Hi,
I am using Bash shell to create some data and these data would be piped out to a file, let say output.txt.
This output.txt I would like to add some extra header information such as comments, descriptions and general information on the text.
I would like to know how could I maintain... (0 Replies)
Hello Friends,
I have got, this output below and i want to extract the name of symlink which is highlighted in red and the path above it highlighted in blue. At the end i want to append path and symlink.
/var/tmp/asirohi/jdk/jre
/var/tmp/asirohi/jdk/jre/.systemPrefs... (3 Replies)
Hi all,
I have space delimated file which look like this
1 2 3 4
5 6 7 8
9 1 0 11
I am using simple awk command to read the second column
awk '{print $2}' input_file
but i got the output like this which also read 10 from the third column
2
6... (8 Replies)
Hi,
Is there a way to write to a txt file each day but retain the header on the file? I'm cat'ing 5 files into one .txt file each day but I want the new data to be written after the first 2 lines which are:
Progname Size Date Owner
----------------------------
Basically I want my new... (4 Replies)
I have a file with very specific column spacing formatting,
I wish to do the following:
awk '{print $1, $2, $3, $4, $5, $6, $19-$7, $20-$8, $21-$9, $10, $11, $12}' merge.pdb > vector.pdb
but the format gets ruined.
I have tried with print -f but to no avail.... (7 Replies)
Hello There...
I have a sample input file ..
number:department:amount
125:Market:125.23
126:Hardware store:434.95
127:Video store:7.45
128:Book store:14.32
129:Gasolline:16.10
I will be doing some manipulations on all the records except the header, but the header should always be... (2 Replies)
I am trying to output all lines in a file where $7 is less than 30. The below code does create a result file, but with all lines in the original file. The original file is tab deliminated is that the problem? Thank you :).
awk 'BEGIN{FS=OFS=","} $7 < 30 {print}' file.txt > result.txt... (3 Replies)
In the awk below I am trying to print only the header lines starting with # or ## and the lines that $7 is PASS and AF= is less than 5%. The awk does execute but returns an empty file and I am not sure what I am doing wrong. Thank you.
file
... (0 Replies)
I've been struggling with this one for quite a while and cannot seem to find a solution for this find/replace scenario. Perhaps I'm getting rusty.
I have a file that contains a number of metrics (exactly 3 fields per line) from a few appliances that are collected in parallel. To identify the... (3 Replies)
02-27-2019
.