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Add specific string to last field of each line in perl based on value

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# 1  
Old 05-27-2016
Add specific string to last field of each line in perl based on value
I am trying to add a condition to the below perl that will capture the GTtag and place a specific string in the last field of each line. The problem is that the GT value used is not right after the tag rather it is a few fields away. The values should always be 0/1 or 1/2 and are in bold in the input. 0/1=het and 1/2=hom. Thank you Smilie.

input
Code:
##
##
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##
##
#CHROM    POS    ID    REF    ALT    QUAL    FILTER    INFO    FORMAT    SAMPLE
chr1    9324670    .    A    G    672.016    PASS    AF=0.528369;AO=148;DP=281;FAO=149;FDP=282;FR=.;FRO=133;FSAF=59;FSAR=90;FSRF=60;FSRR=73;FWDB=0.00343606;FXX=0;HRUN=1;LEN=1;MLLD=155.207;OALT=G;OID=.;OMAPALT=G;OPOS=9324670;OREF=A;PB=0.5;PBP=1;QD=9.53214;RBI=0.00594431;REFB=-0.0181827;REVB=0.00485061;RO=130;SAF=59;SAR=89;SRF=57;SRR=73;SSEN=0;SSEP=0;SSSB=-0.0352973;STB=0.526882;STBP=0.323;TYPE=snp;VARB=0.0184938;ANN=H6PD    GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR    0/1:527:281:282:130:133:148:149:0.528369:89:59:57:73:90:59:60:73 GOOD 282 reads
chr1    10318652    .    C    G    360.217    PASS    AF=0.566929;AO=72;DP=129;FAO=72;FDP=127;FR=.;FRO=55;FSAF=36;FSAR=36;FSRF=31;FSRR=24;FWDB=0.00760676;FXX=0.0155027;HRUN=2;LEN=1;MLLD=115.62;OALT=G;OID=.;OMAPALT=G;OPOS=10318652;OREF=C;PB=0.5;PBP=1;QD=11.3454;RBI=0.0125905;REFB=-0.0312889;REVB=-0.0100329;RO=55;SAF=36;SAR=36;SRF=31;SRR=24;SSEN=0;SSEP=0;SSSB=-0.0505108;STB=0.527551;STBP=0.492;TYPE=snp;VARB=0.0181889;ANN=KIF1B    GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR    1/1:203:129:127:55:55:72:72:0.566929:36:36:31:24:36:36:31:24 GOOD 127 reads
chr1    10355834    .    C    T    504.995    PASS    AF=0.456747;AO=132;DP=290;FAO=132;FDP=289;FR=.;FRO=157;FSAF=56;FSAR=76;FSRF=85;FSRR=72;FWDB=0.0634576;FXX=0.00344816;HRUN=2;LEN=1;MLLD=58.7971;OALT=T;OID=.;OMAPALT=T;OPOS=10355834;OREF=C;PB=0.5;PBP=1;QD=6.98956;RBI=0.0644815;REFB=0.00590624;REVB=-0.0114455;RO=156;SAF=56;SAR=76;SRF=85;SRR=71;SSEN=0;SSEP=0;SSSB=-0.118565;STB=0.563872;STBP=0.047;TYPE=snp;VARB=-0.00678859;ANN=KIF1B    GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR    0/1:504:290:289:156:157:132:132:0.456747:76:56:85:71:76:56:85:72 GOOD 289 reads
chr1    11090916    .    C    A    1855.57    PASS    AF=1;AO=193;DP=193;FAO=194;FDP=194;FR=.;FRO=0;FSAF=96;FSAR=98;FSRF=0;FSRR=0;FWDB=0.0243175;FXX=0;HRUN=1;LEN=1;MLLD=207.14;OALT=A;OID=.;OMAPALT=A;OPOS=11090916;OREF=C;PB=0.5;PBP=1;QD=38.2592;RBI=0.048476;REFB=0;REVB=0.0419355;RO=0;SAF=95;SAR=98;SRF=0;SRR=0;SSEN=0;SSEP=0;SSSB=4.54468e-08;STB=0.5;STBP=1;TYPE=snp;VARB=3.87852e-05;ANN=MASP2    GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR    1/1:88:193:194:0:0:193:194:1:98:95:0:0:98:96:0:0 GOOD 194 reads
chr1    213068404    .    T    C    70.4374    PASS    AF=0.435897;AO=17;DP=39;FAO=17;FDP=39;FR=.;FRO=22;FSAF=16;FSAR=1;FSRF=11;FSRR=11;FWDB=-0.000611735;FXX=0;HRUN=1;LEN=1;MLLD=243.519;OALT=C;OID=.;OMAPALT=C;OPOS=213068404;OREF=T;PB=0.5;PBP=1;QD=7.22435;RBI=0.023516;REFB=0.00205571;REVB=0.023508;RO=22;SAF=16;SAR=1;SRF=11;SRR=11;SSEN=0;SSEP=0;SSSB=0.630793;STB=0.87614;STBP=0.001;TYPE=snp;VARB=-0.00167889;ANN=FLVCR1    GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR    0/1:70:39:39:22:22:17:17:0.435897:1:16:11:11:1:16:11:11 STRAND BIAS 39 reads

desired output
Code:
##
##
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##
##
#CHROM    POS    ID    REF    ALT    QUAL    FILTER    INFO    FORMAT    SAMPLE
chr1    9324670    .    A    G    672.016    PASS    AF=0.528369;AO=148;DP=281;FAO=149;FDP=282;FR=.;FRO=133;FSAF=59;FSAR=90;FSRF=60;FSRR=73;FWDB=0.00343606;FXX=0;HRUN=1;LEN=1;MLLD=155.207;OALT=G;OID=.;OMAPALT=G;OPOS=9324670;OREF=A;PB=0.5;PBP=1;QD=9.53214;RBI=0.00594431;REFB=-0.0181827;REVB=0.00485061;RO=130;SAF=59;SAR=89;SRF=57;SRR=73;SSEN=0;SSEP=0;SSSB=-0.0352973;STB=0.526882;STBP=0.323;TYPE=snp;VARB=0.0184938;ANN=H6PD    GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR    0/1:527:281:282:130:133:148:149:0.528369:89:59:57:73:90:59:60:73 GOOD 282 reads het
chr1    10318652    .    C    G    360.217    PASS    AF=0.566929;AO=72;DP=129;FAO=72;FDP=127;FR=.;FRO=55;FSAF=36;FSAR=36;FSRF=31;FSRR=24;FWDB=0.00760676;FXX=0.0155027;HRUN=2;LEN=1;MLLD=115.62;OALT=G;OID=.;OMAPALT=G;OPOS=10318652;OREF=C;PB=0.5;PBP=1;QD=11.3454;RBI=0.0125905;REFB=-0.0312889;REVB=-0.0100329;RO=55;SAF=36;SAR=36;SRF=31;SRR=24;SSEN=0;SSEP=0;SSSB=-0.0505108;STB=0.527551;STBP=0.492;TYPE=snp;VARB=0.0181889;ANN=KIF1B    GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR    1/1:203:129:127:55:55:72:72:0.566929:36:36:31:24:36:36:31:24 GOOD 127 reads hom
chr1    10355834    .    C    T    504.995    PASS    AF=0.456747;AO=132;DP=290;FAO=132;FDP=289;FR=.;FRO=157;FSAF=56;FSAR=76;FSRF=85;FSRR=72;FWDB=0.0634576;FXX=0.00344816;HRUN=2;LEN=1;MLLD=58.7971;OALT=T;OID=.;OMAPALT=T;OPOS=10355834;OREF=C;PB=0.5;PBP=1;QD=6.98956;RBI=0.0644815;REFB=0.00590624;REVB=-0.0114455;RO=156;SAF=56;SAR=76;SRF=85;SRR=71;SSEN=0;SSEP=0;SSSB=-0.118565;STB=0.563872;STBP=0.047;TYPE=snp;VARB=-0.00678859;ANN=KIF1B    GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR    0/1:504:290:289:156:157:132:132:0.456747:76:56:85:71:76:56:85:72 GOOD 289 reads het
chr1    11090916    .    C    A    1855.57    PASS    AF=1;AO=193;DP=193;FAO=194;FDP=194;FR=.;FRO=0;FSAF=96;FSAR=98;FSRF=0;FSRR=0;FWDB=0.0243175;FXX=0;HRUN=1;LEN=1;MLLD=207.14;OALT=A;OID=.;OMAPALT=A;OPOS=11090916;OREF=C;PB=0.5;PBP=1;QD=38.2592;RBI=0.048476;REFB=0;REVB=0.0419355;RO=0;SAF=95;SAR=98;SRF=0;SRR=0;SSEN=0;SSEP=0;SSSB=4.54468e-08;STB=0.5;STBP=1;TYPE=snp;VARB=3.87852e-05;ANN=MASP2    GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR    1/1:88:193:194:0:0:193:194:1:98:95:0:0:98:96:0:0 GOOD 194 reads hom
chr1    213068404    .    T    C    70.4374    PASS    AF=0.435897;AO=17;DP=39;FAO=17;FDP=39;FR=.;FRO=22;FSAF=16;FSAR=1;FSRF=11;FSRR=11;FWDB=-0.000611735;FXX=0;HRUN=1;LEN=1;MLLD=243.519;OALT=C;OID=.;OMAPALT=C;OPOS=213068404;OREF=T;PB=0.5;PBP=1;QD=7.22435;RBI=0.023516;REFB=0.00205571;REVB=0.023508;RO=22;SAF=16;SAR=1;SRF=11;SRR=11;SSEN=0;SSEP=0;SSSB=0.630793;STB=0.87614;STBP=0.001;TYPE=snp;VARB=-0.00167889;ANN=FLVCR1    GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR    0/1:70:39:39:22:22:17:17:0.435897:1:16:11:11:1:16:11:11 STRAND BIAS 39 reads het

perl
Code:
perl -ple '/^[^#].*FDP=(\d+);.*STB=(\d+\.\d+);.*GT=(\d+);  ($9:*)= 0/1?="het",= 1/1?="hom"/ and $_.=($2 >= 0.8?" STRAND BIAS ":" GOOD ").$1." reads"' input > results.txt

# 2  
Old 05-27-2016
Quote:
The values should always be 0/1 or 1/2 and are in bold in the input . 0/1=het and 1/2=hom
You said: "1/2 equals hom", however, in your desired output 1/1 gets hom, and 1/2 is nowhere to be found.

Here's a line of Perl that produces what you posted as desired output, based on what you posted as input:

Code:
perl -ple 'BEGIN{%h=qw(0/1 het 1/1 hom)}; /([01]\/1)/ and $_ .= " $h{$1}"'  input > results.txt

This User Gave Thanks to Aia For This Post:
cmccabe
# 3  
Old 05-27-2016
I apologize for the typo.... it may be easier to include all 0/0 or 1/1 or 2/2 as hom. The other condition is 0/1 or 1/2 is het . I think these are all the possibilities. Thank you Smilie.
# 4  
Old 05-27-2016
Quote:
Originally Posted by cmccabe
I apologize for the typo.... it may be easier to include all 0/0 or 1/1 or 2/2 as hom. The other condition is 0/1 or 1/2 is het . I think these are all the possibilities. Thank you Smilie.
Modify it, accordingly.

Code:
perl -ple 'BEGIN{%h=qw(0/0 hom 0/1 het 1/1 hom 1/2 het 2/2 hom)} /([0-2]\/[0-2])/ and $_ .=" $h{$1}"'  input > results.txt

This User Gave Thanks to Aia For This Post:
cmccabe
# 5  
Old 05-27-2016
If you showed us a representative sample of your real input, you could also try using awk (or, on Solaris/SunOS systems, nawk or /usr/xpg4/bin/awk):
Code:
awk '$10~"^[012]"{$0=$0($10~"^(0/0|1/1|2/2)"?" hom":" het")}1' input > results.txt

This User Gave Thanks to Don Cragun For This Post:
cmccabe
# 6  
Old 05-28-2016
Thank you very much Smilie
# 7  
Old 06-28-2016
The below perl from @Aia works great and produces the desired result, but I don't think I understand how it works. Is it possible to explain a little, maybe that will help. Thank you Smilie.

Code:
perl -ple 'BEGIN{%h=qw(0/0 hom 0/1 het 1/1 hom 1/2 het 2/2 hom)} /([0-2]\/[0-2])/ and $_ .=" $h{$1}"'

For example, how does STB get calculated or the reads extracted?

The input file is the one in the post. I have a follow-up question but I want to try and understand so I can make an attempt at a perl code. Thank you.

Followup question:
The below perl produces the current results. In the desired results the last fields below are added and need to be tab deliniated. The value in front of the string "score" is caculated from $6 or QUAL. That calculation is $6/33.

Code:
GOOD 282 reads het 20 score  (672.016/33) no decimal, rounded up
GOOD 127 reads hom 11 score  (360.217/33) no decimal, rounded up
GOOD 289 reads het 15 score  (504.995/33) no decimal, rounded up
GOOD 194 reads hom 56 score  (1855.57/33) no decimal, rounded up
STRAND BIAS 39 reads het 2 score  (70.4374/33) no decimal, rounded up


Code:
perl -ple 'BEGIN{%h=qw(0/0 hom 0/1 het 1/1 hom 1/2 het 2/2 hom)} /([0-2]\/[0-2])/ and $_ .=" $h{$1}"'  input > results.txt


input
Code:
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
#CHROM    POS    ID    REF    ALT    QUAL    FILTER    INFO    FORMAT    SAMPLE
chr1    9324670    .    A    G    672.016    PASS    AF=0.528369;AO=148;DP=281;FAO=149;FDP=282;FR=.;FRO=133;FSAF=59;FSAR=90;FSRF=60;FSRR=73;FWDB=0.00343606;FXX=0;HRUN=1;LEN=1;MLLD=155.207;OALT=G;OID=.;OMAPALT=G;OPOS=9324670;OREF=A;PB=0.5;PBP=1;QD=9.53214;RBI=0.00594431;REFB=-0.0181827;REVB=0.00485061;RO=130;SAF=59;SAR=89;SRF=57;SRR=73;SSEN=0;SSEP=0;SSSB=-0.0352973;STB=0.526882;STBP=0.323;TYPE=snp;VARB=0.0184938;ANN=H6PD    GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR    0/1:527:281:282:130:133:148:149:0.528369:89:59:57:73:90:59:60:73
chr1    10318652    .    C    G    360.217    PASS    AF=0.566929;AO=72;DP=129;FAO=72;FDP=127;FR=.;FRO=55;FSAF=36;FSAR=36;FSRF=31;FSRR=24;FWDB=0.00760676;FXX=0.0155027;HRUN=2;LEN=1;MLLD=115.62;OALT=G;OID=.;OMAPALT=G;OPOS=10318652;OREF=C;PB=0.5;PBP=1;QD=11.3454;RBI=0.0125905;REFB=-0.0312889;REVB=-0.0100329;RO=55;SAF=36;SAR=36;SRF=31;SRR=24;SSEN=0;SSEP=0;SSSB=-0.0505108;STB=0.527551;STBP=0.492;TYPE=snp;VARB=0.0181889;ANN=KIF1B    GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR    1/1:203:129:127:55:55:72:72:0.566929:36:36:31:24:36:36:31:24
chr1    10355834    .    C    T    504.995    PASS    AF=0.456747;AO=132;DP=290;FAO=132;FDP=289;FR=.;FRO=157;FSAF=56;FSAR=76;FSRF=85;FSRR=72;FWDB=0.0634576;FXX=0.00344816;HRUN=2;LEN=1;MLLD=58.7971;OALT=T;OID=.;OMAPALT=T;OPOS=10355834;OREF=C;PB=0.5;PBP=1;QD=6.98956;RBI=0.0644815;REFB=0.00590624;REVB=-0.0114455;RO=156;SAF=56;SAR=76;SRF=85;SRR=71;SSEN=0;SSEP=0;SSSB=-0.118565;STB=0.563872;STBP=0.047;TYPE=snp;VARB=-0.00678859;ANN=KIF1B    GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR    0/1:504:290:289:156:157:132:132:0.456747:76:56:85:71:76:56:85:72
chr1    11090916    .    C    A    1855.57    PASS    AF=1;AO=193;DP=193;FAO=194;FDP=194;FR=.;FRO=0;FSAF=96;FSAR=98;FSRF=0;FSRR=0;FWDB=0.0243175;FXX=0;HRUN=1;LEN=1;MLLD=207.14;OALT=A;OID=.;OMAPALT=A;OPOS=11090916;OREF=C;PB=0.5;PBP=1;QD=38.2592;RBI=0.048476;REFB=0;REVB=0.0419355;RO=0;SAF=95;SAR=98;SRF=0;SRR=0;SSEN=0;SSEP=0;SSSB=4.54468e-08;STB=0.5;STBP=1;TYPE=snp;VARB=3.87852e-05;ANN=MASP2    GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR    1/1:88:193:194:0:0:193:194:1:98:95:0:0:98:96:0:0
chr1    213068404    .    T    C    70.4374    PASS    AF=0.435897;AO=17;DP=39;FAO=17;FDP=39;FR=.;FRO=22;FSAF=16;FSAR=1;FSRF=11;FSRR=11;FWDB=-0.000611735;FXX=0;HRUN=1;LEN=1;MLLD=243.519;OALT=C;OID=.;OMAPALT=C;OPOS=213068404;OREF=T;PB=0.5;PBP=1;QD=7.22435;RBI=0.023516;REFB=0.00205571;REVB=0.023508;RO=22;SAF=16;SAR=1;SRF=11;SRR=11;SSEN=0;SSEP=0;SSSB=0.630793;STB=0.87614;STBP=0.001;TYPE=snp;VARB=-0.00167889;ANN=FLVCR1    GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR    0/1:70:39:39:22:22:17:17:0.435897:1:16:11:11:1:16:11:11


current results
Code:
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
#CHROM    POS    ID    REF    ALT    QUAL    FILTER    INFO    FORMAT    SAMPLE
chr1    9324670    .    A    G    672.016    PASS    AF=0.528369;AO=148;DP=281;FAO=149;FDP=282;FR=.;FRO=133;FSAF=59;FSAR=90;FSRF=60;FSRR=73;FWDB=0.00343606;FXX=0;HRUN=1;LEN=1;MLLD=155.207;OALT=G;OID=.;OMAPALT=G;OPOS=9324670;OREF=A;PB=0.5;PBP=1;QD=9.53214;RBI=0.00594431;REFB=-0.0181827;REVB=0.00485061;RO=130;SAF=59;SAR=89;SRF=57;SRR=73;SSEN=0;SSEP=0;SSSB=-0.0352973;STB=0.526882;STBP=0.323;TYPE=snp;VARB=0.0184938;ANN=H6PD    GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR    0/1:527:281:282:130:133:148:149:0.528369:89:59:57:73:90:59:60:73 GOOD 282 reads het
chr1    10318652    .    C    G    360.217    PASS    AF=0.566929;AO=72;DP=129;FAO=72;FDP=127;FR=.;FRO=55;FSAF=36;FSAR=36;FSRF=31;FSRR=24;FWDB=0.00760676;FXX=0.0155027;HRUN=2;LEN=1;MLLD=115.62;OALT=G;OID=.;OMAPALT=G;OPOS=10318652;OREF=C;PB=0.5;PBP=1;QD=11.3454;RBI=0.0125905;REFB=-0.0312889;REVB=-0.0100329;RO=55;SAF=36;SAR=36;SRF=31;SRR=24;SSEN=0;SSEP=0;SSSB=-0.0505108;STB=0.527551;STBP=0.492;TYPE=snp;VARB=0.0181889;ANN=KIF1B    GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR    1/1:203:129:127:55:55:72:72:0.566929:36:36:31:24:36:36:31:24 GOOD 127 reads hom
chr1    10355834    .    C    T    504.995    PASS    AF=0.456747;AO=132;DP=290;FAO=132;FDP=289;FR=.;FRO=157;FSAF=56;FSAR=76;FSRF=85;FSRR=72;FWDB=0.0634576;FXX=0.00344816;HRUN=2;LEN=1;MLLD=58.7971;OALT=T;OID=.;OMAPALT=T;OPOS=10355834;OREF=C;PB=0.5;PBP=1;QD=6.98956;RBI=0.0644815;REFB=0.00590624;REVB=-0.0114455;RO=156;SAF=56;SAR=76;SRF=85;SRR=71;SSEN=0;SSEP=0;SSSB=-0.118565;STB=0.563872;STBP=0.047;TYPE=snp;VARB=-0.00678859;ANN=KIF1B    GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR    0/1:504:290:289:156:157:132:132:0.456747:76:56:85:71:76:56:85:72 GOOD 289 reads het
chr1    11090916    .    C    A    1855.57    PASS    AF=1;AO=193;DP=193;FAO=194;FDP=194;FR=.;FRO=0;FSAF=96;FSAR=98;FSRF=0;FSRR=0;FWDB=0.0243175;FXX=0;HRUN=1;LEN=1;MLLD=207.14;OALT=A;OID=.;OMAPALT=A;OPOS=11090916;OREF=C;PB=0.5;PBP=1;QD=38.2592;RBI=0.048476;REFB=0;REVB=0.0419355;RO=0;SAF=95;SAR=98;SRF=0;SRR=0;SSEN=0;SSEP=0;SSSB=4.54468e-08;STB=0.5;STBP=1;TYPE=snp;VARB=3.87852e-05;ANN=MASP2    GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR    1/1:88:193:194:0:0:193:194:1:98:95:0:0:98:96:0:0 GOOD 194 reads hom
chr1    213068404    .    T    C    70.4374    PASS    AF=0.435897;AO=17;DP=39;FAO=17;FDP=39;FR=.;FRO=22;FSAF=16;FSAR=1;FSRF=11;FSRR=11;FWDB=-0.000611735;FXX=0;HRUN=1;LEN=1;MLLD=243.519;OALT=C;OID=.;OMAPALT=C;OPOS=213068404;OREF=T;PB=0.5;PBP=1;QD=7.22435;RBI=0.023516;REFB=0.00205571;REVB=0.023508;RO=22;SAF=16;SAR=1;SRF=11;SRR=11;SSEN=0;SSEP=0;SSSB=0.630793;STB=0.87614;STBP=0.001;TYPE=snp;VARB=-0.00167889;ANN=FLVCR1    GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR    0/1:70:39:39:22:22:17:17:0.435897:1:16:11:11:1:16:11:11 STRAND BIAS 39 reads het


desired results
Code:
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
#CHROM    POS    ID    REF    ALT    QUAL    FILTER    INFO    FORMAT    SAMPLE
chr1    9324670    .    A    G    672.016    PASS    AF=0.528369;AO=148;DP=281;FAO=149;FDP=282;FR=.;FRO=133;FSAF=59;FSAR=90;FSRF=60;FSRR=73;FWDB=0.00343606;FXX=0;HRUN=1;LEN=1;MLLD=155.207;OALT=G;OID=.;OMAPALT=G;OPOS=9324670;OREF=A;PB=0.5;PBP=1;QD=9.53214;RBI=0.00594431;REFB=-0.0181827;REVB=0.00485061;RO=130;SAF=59;SAR=89;SRF=57;SRR=73;SSEN=0;SSEP=0;SSSB=-0.0352973;STB=0.526882;STBP=0.323;TYPE=snp;VARB=0.0184938;ANN=H6PD    GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR    0/1:527:281:282:130:133:148:149:0.528369:89:59:57:73:90:59:60:73 GOOD 282 reads het 20 score
chr1    10318652    .    C    G    360.217    PASS    AF=0.566929;AO=72;DP=129;FAO=72;FDP=127;FR=.;FRO=55;FSAF=36;FSAR=36;FSRF=31;FSRR=24;FWDB=0.00760676;FXX=0.0155027;HRUN=2;LEN=1;MLLD=115.62;OALT=G;OID=.;OMAPALT=G;OPOS=10318652;OREF=C;PB=0.5;PBP=1;QD=11.3454;RBI=0.0125905;REFB=-0.0312889;REVB=-0.0100329;RO=55;SAF=36;SAR=36;SRF=31;SRR=24;SSEN=0;SSEP=0;SSSB=-0.0505108;STB=0.527551;STBP=0.492;TYPE=snp;VARB=0.0181889;ANN=KIF1B    GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR    1/1:203:129:127:55:55:72:72:0.566929:36:36:31:24:36:36:31:24 GOOD 127 reads hom 11 score
chr1    10355834    .    C    T    504.995    PASS    AF=0.456747;AO=132;DP=290;FAO=132;FDP=289;FR=.;FRO=157;FSAF=56;FSAR=76;FSRF=85;FSRR=72;FWDB=0.0634576;FXX=0.00344816;HRUN=2;LEN=1;MLLD=58.7971;OALT=T;OID=.;OMAPALT=T;OPOS=10355834;OREF=C;PB=0.5;PBP=1;QD=6.98956;RBI=0.0644815;REFB=0.00590624;REVB=-0.0114455;RO=156;SAF=56;SAR=76;SRF=85;SRR=71;SSEN=0;SSEP=0;SSSB=-0.118565;STB=0.563872;STBP=0.047;TYPE=snp;VARB=-0.00678859;ANN=KIF1B    GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR    0/1:504:290:289:156:157:132:132:0.456747:76:56:85:71:76:56:85:72 GOOD 289 reads het 15 score
chr1    11090916    .    C    A    1855.57    PASS    AF=1;AO=193;DP=193;FAO=194;FDP=194;FR=.;FRO=0;FSAF=96;FSAR=98;FSRF=0;FSRR=0;FWDB=0.0243175;FXX=0;HRUN=1;LEN=1;MLLD=207.14;OALT=A;OID=.;OMAPALT=A;OPOS=11090916;OREF=C;PB=0.5;PBP=1;QD=38.2592;RBI=0.048476;REFB=0;REVB=0.0419355;RO=0;SAF=95;SAR=98;SRF=0;SRR=0;SSEN=0;SSEP=0;SSSB=4.54468e-08;STB=0.5;STBP=1;TYPE=snp;VARB=3.87852e-05;ANN=MASP2    GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR    1/1:88:193:194:0:0:193:194:1:98:95:0:0:98:96:0:0 GOOD 194 reads hom 56 score
chr1    213068404    .    T    C    70.4374    PASS    AF=0.435897;AO=17;DP=39;FAO=17;FDP=39;FR=.;FRO=22;FSAF=16;FSAR=1;FSRF=11;FSRR=11;FWDB=-0.000611735;FXX=0;HRUN=1;LEN=1;MLLD=243.519;OALT=C;OID=.;OMAPALT=C;OPOS=213068404;OREF=T;PB=0.5;PBP=1;QD=7.22435;RBI=0.023516;REFB=0.00205571;REVB=0.023508;RO=22;SAF=16;SAR=1;SRF=11;SRR=11;SSEN=0;SSEP=0;SSSB=0.630793;STB=0.87614;STBP=0.001;TYPE=snp;VARB=-0.00167889;ANN=FLVCR1    GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR    0/1:70:39:39:22:22:17:17:0.435897:1:16:11:11:1:16:11:11 STRAND BIAS 39 reads het 2 score

Last edited by cmccabe; 06-28-2016 at 03:50 PM.. Reason: added edit and followup ?
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