##fileformat=VCFv4.1
##FILTER=<ID=DP,Description="Less that 1/3 mutant alleles were high quality.">
##FILTER=<ID=RP,Description="Coverage was <9 and no mutant alleles in the first 2/3 of a read (within given boundaries)">
##FILTER=<ID=MN,Description="More than the set proportion of high quality mutant alleles in the matched normal.">
##FILTER=<ID=UM,Description="More than the set proportion of mutant alleles were found in at least 'n' unmatched normal samples.">
##FILTER=<ID=PT,Description="Mutant alleles all on one direction of read (1rd allowed on opposite strand) and in second half of the read. Second half of read contains the motif GGC[AT]G in sequenced orientation and the mean base quality of all bases after the motif was less than the required value.">
##FILTER=<ID=MQ,Description="Mean mapping quality of the mutant allele reads was less than the required value.">
##FILTER=<ID=SR,Description="Position falls within 5 bases of a simple repeat.">
##FILTER=<ID=CR,Description="Position falls within a centromeric repeat.">
##FILTER=<ID=PH,Description="Mutant reads were mostly on one strand, and mean mut base quality was less than the set requirement.">
##FILTER=<ID=TI,Description="More than the set percentage of reads covering this position contained an indel according to mapping.">
##FILTER=<ID=SRP,Description="More than the set percentage of reads contain the mutant allele at the same position.">
##FILTER=<ID=HSD,Description="Position falls within a high sequencing depth region as defined by top 1 pct of 1k genomes.">
##FILTER=<ID=AN,Description="Position could not be annotated against a transcript.">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=AA,Number=1,Type=Integer,Description="Reads presenting a A for this position">
##FORMAT=<ID=CA,Number=1,Type=Integer,Description="Reads presenting a C for this position">
##FORMAT=<ID=GA,Number=1,Type=Integer,Description="Reads presenting a G for this position">
##FORMAT=<ID=TA,Number=1,Type=Integer,Description="Reads presenting a T for this position">
##FORMAT=<ID=PM,Number=1,Type=Float,Description="Proportion of mut allele">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=MP,Number=1,Type=Float,Description="Sum of CaVEMan somatic genotype probabilities">
##INFO=<ID=GP,Number=1,Type=Float,Description="Sum of CaVEMan germline genotype probabilities">
##INFO=<ID=TG,Number=1,Type=String,Description="Most probable genotype as called by CaVEMan">
##INFO=<ID=TP,Number=1,Type=Float,Description="Probability of most probable genotype as called by CaVEMan">
##INFO=<ID=SG,Number=1,Type=String,Description="2nd most probable genotype as called by CaVEMan">
##INFO=<ID=SP,Number=1,Type=Float,Description="Probability of 2nd most probable genotype as called by CaVEMan">
##INFO=<ID=DS,Number=.,Type=String,Description="DBSnp ID of known SNP">
##INFO=<ID=CA,Number=0,Type=Flag,Description="Position could not be annotated to a coding region of a transcript.">
##INFO=<ID=SNP,Number=0,Type=Flag,Description="Position matches a dbSNP entry.">
##INFO=<ID=VD,Number=1,Type=String,Description="Vagrent Default Annotation">
##INFO=<ID=VW,Number=1,Type=String,Description="Vagrent Most Deleterious Annotation">
##SAMPLE=<ID=NORMAL,Description="Normal",Accession=1474009,CGP_Project=54,Platform=HiSeq,Protocol=pulldown,SampleName=PD5924b,Source=COSMIC_SAMPLE_ID>
##SAMPLE=<ID=TUMOUR,Description="Mutant",Accession=1287381,CGP_Project=786,Platform=HiSeq,Protocol=pulldown,SampleName=201T,Source=COSMIC_SAMPLE_ID>
##cavemanParams="NORMAL_CONTAMINATION=0.0;REF_BIAS=0.950000;MUT_RATE=0.000006;SNP_RATE=0.001000;MUT_CUTOFF=0.80;SNP_CUTOFF=0.95;MAX_READ_DEPTH_PER_SAMPLE=500"
##cavemanVersion=V|0_5_1|31_03_11
##cgpAnalysisProc_20130323.1=934452
##cgpAnalysisProc_20130326.1=934666
##cgpAnalysisProc_20130326.2=950997
##contig=<ID=11,assembly=GRCh37,length=135006516,species=HUMAN>
##contig=<ID=21,assembly=GRCh37,length=48129895,species=HUMAN>
##contig=<ID=7,assembly=GRCh37,length=159138663,species=HUMAN>
##contig=<ID=Y,assembly=GRCh37,length=59373566,species=HUMAN>
##contig=<ID=17,assembly=GRCh37,length=81195210,species=HUMAN>
##contig=<ID=2,assembly=GRCh37,length=243199373,species=HUMAN>
##contig=<ID=22,assembly=GRCh37,length=51304566,species=HUMAN>
##contig=<ID=1,assembly=GRCh37,length=249250621,species=HUMAN>
##contig=<ID=18,assembly=GRCh37,length=78077248,species=HUMAN>
##contig=<ID=16,assembly=GRCh37,length=90354753,species=HUMAN>
##contig=<ID=13,assembly=GRCh37,length=115169878,species=HUMAN>
##contig=<ID=6,assembly=GRCh37,length=171115067,species=HUMAN>
##contig=<ID=X,assembly=GRCh37,length=155270560,species=HUMAN>
##contig=<ID=3,assembly=GRCh37,length=198022430,species=HUMAN>
##contig=<ID=MT,assembly=GRCh37,length=16569,species=HUMAN>
##contig=<ID=9,assembly=GRCh37,length=141213431,species=HUMAN>
##contig=<ID=12,assembly=GRCh37,length=133851895,species=HUMAN>
##contig=<ID=20,assembly=GRCh37,length=63025520,species=HUMAN>
##contig=<ID=14,assembly=GRCh37,length=107349540,species=HUMAN>
##contig=<ID=15,assembly=GRCh37,length=102531392,species=HUMAN>
##contig=<ID=8,assembly=GRCh37,length=146364022,species=HUMAN>
##contig=<ID=4,assembly=GRCh37,length=191154276,species=HUMAN>
##contig=<ID=19,assembly=GRCh37,length=59128983,species=HUMAN>
##contig=<ID=10,assembly=GRCh37,length=135534747,species=HUMAN>
##contig=<ID=5,assembly=GRCh37,length=180915260,species=HUMAN>
##fileDate=20130223
##reference=genome.fa
##source_20130323.1=CavemanMerge2Vcf.pl
##source_20130326.1=VcfAnnotate.pl
##vcfProcessLog_20130323.1=<InputVCF=<tmp.tab>,InputVCFSource=<CavemanMerge2Vcf.pl>,InputVCFVer=<1.1>,InputVCFParam=<rs=595026967,n=1474009,np=pulldown,tl=HiSeq,r=genome.fa,tj=786,tp=pulldown,v=GRCh37,s=HUMAN,nl=HiSeq,p=934452,rt=595049500,nj=54,i=tmp.tab,t=1287381>>
##vcfProcessLog_20130326.1=<InputVCF=<split.1>,InputVCFSource=<FlagCaVEManVCF.pl>,InputVCFVer=<0.16.1>,InputVCFParam=<sp=.,db=pulldown.bdb,um=caveman_unmatched,u=549409.1,h=.,g=.,f=split.1,t=PULLDOWN,loud=.,n=wt.bam,m=mt.bam,v=flag.to.vcf.convert.ini,s=HUMAN,l=2000,ab=vagrent,p=934666,c=flag.vcf.config.ini,b=37,optStr=flag.to.vcf.convert.ini,idx=.,o=split.flag.1>>
##vcfProcessLog_20130326.2=<InputVCF=<429316.v1.cave.flag.vcf.gz>,InputVCFSource=<VcfAnnotate.pl>,InputVCFVer=<0.6.3>,InputVCFParam=<gene_footprints=gene_regions.bed.gz,ensembl=58,species=HUMAN,genome=GRCh37>>
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	TUMOUR
1	13079	595026967	C	G	.	MQ;AN	DP=135;MP=1.0e+00;GP=1.7e-17;TG=CC/CCCCG;TP=1.0e+00;SG=CC/CCCCC;SP=4.2e-03	GT:AA:CA:GA:TA:PM	0/0:0:65:0:0:0.0e+00	0/1:0:65:5:0:7.1e-02
1	13418	595026968	G	A	.	UM;MQ;AN	DP=311;MP=1.0e+00;GP=6.2e-39;TG=GG/AGGGG;TP=1.0e+00;SG=GG/AAGGG;SP=3.9e-06	GT:AA:CA:GA:TA:PM	0/0:0:0:139:0:0.0e+00	0/1:36:0:136:0:2.1e-01
1	15072	595026969	G	C	.	MQ;AN	DP=150;MP=1.0e+00;GP=6.8e-26;TG=GG/CCGGG;TP=9.9e-01;SG=GG/CGGGG;SP=6.4e-03	GT:AA:CA:GA:TA:PM	0/0:0:0:94:0:0.0e+00	0/1:0:21:35:0:3.8e-01
1	16957	595026970	G	T	.	MQ;AN	DP=83;MP=1.0e+00;GP=5.8e-10;TG=GG/GGGTT;TP=5.9e-01;SG=GG/GGTTT;SP=4.1e-01	GT:AA:CA:GA:TA:PM	0/0:0:0:39:0:0.0e+00	0/1:0:0:23:21:4.8e-01
1	17594	595026971	C	T	.	AN	DP=106;MP=1.0e+00;GP=1.0e-13;TG=CC/CCCCT;TP=1.0e+00;SG=CC/CCCTT;SP=3.0e-04	GT:AA:CA:GA:TA:PM	0/0:0:52:0:0:0.0e+00	0/1:0:47:0:7:1.3e-01
1	17626	595026972	G	A	.	AN	DP=141;MP=1.0e+00;GP=1.7e-19;TG=GG/AGGGG;TP=1.0e+00;SG=GG/AAGGG;SP=8.7e-05	GT:AA:CA:GA:TA:PM	0/0:0:0:72:0:0.0e+00	0/1:10:0:59:0:1.4e-01
1	63697	595026973	T	C	.	UM;AN	DP=407;MP=1.0e+00;GP=1.1e-11;TG=TT/CCCTT;TP=1.0e+00;SG=TT/CCTTT;SP=7.5e-06	GT:AA:CA:GA:TA:PM	0/0:0:0:0:45:0.0e+00	0/1:0:191:0:171:5.3e-01
1	129315	595026974	A	G	.	UM;MQ;AN	DP=288;MP=1.0e+00;GP=2.3e-09;TG=AA/AAAAG;TP=1.0e+00;SG=AG/AAAAG;SP=2.3e-09	GT:AA:CA:GA:TA:PM	0/0:37:0:0:0:0.0e+00	0/1:220:0:31:0:1.2e-01
1	753277	595026975	G	A	.	MQ;AN	DP=176;MP=1.0e+00;GP=2.7e-34;TG=GG/AGGGG;TP=1.0e+00;SG=GG/AAGGG;SP=1.0e-03	GT:AA:CA:GA:TA:PM	0/0:0:0:123:0:0.0e+00	0/1:8:0:45:0:1.5e-01
1	809091	595026976	A	G	.	UM;MQ;AN	DP=494;MP=9.8e-01;GP=2.2e-51;TG=AA/AAAAG;TP=9.8e-01;SG=AA/AAAAA;SP=2.4e-02	GT:AA:CA:GA:TA:PM	0/0:182:0:0:0:0.0e+00	0/1:298:0:14:0:4.5e-02
1	809261	595026977	C	T	.	UM;MQ;AN	DP=435;MP=1.0e+00;GP=1.8e-28;TG=CC/CCCCT;TP=1.0e+00;SG=CC/CCCCC;SP=1.0e-19	GT:AA:CA:GA:TA:PM	0/0:0:103:0:0:0.0e+00	0/1:0:310:0:22:6.6e-02
1	809319	595026978	C	T	.	UM;MQ;AN	DP=364;MP=1.0e+00;GP=3.6e-08;TG=CC/CCCCT;TP=1.0e+00;SG=CT/CCCCT;SP=3.6e-08	GT:AA:CA:GA:TA:PM	0/0:0:33:0:0:0.0e+00	0/1:0:300:0:31:9.4e-02
1	809351	595026979	T	G	.	PH;DP;AN	DP=298;MP=9.9e-01;GP=2.5e-16;TG=TT/GTTTT;TP=9.9e-01;SG=TT/TTTTT;SP=8.3e-03	GT:AA:CA:GA:TA:PM	0/0:0:0:0:61:0.0e+00	0/1:0:0:22:215:9.3e-02
1	809361	595026980	A	C	.	PH;DP;AN	DP=352;MP=1.0e+00;GP=4.0e-22;TG=AA/AAAAC;TP=1.0e+00;SG=AA/AAAAA;SP=2.2e-08	GT:AA:CA:GA:TA:PM	0/0:81:0:0:0:0.0e+00	0/1:250:21:0:0:7.7e-02
1	874865	595026981	T	C	.	TI	DP=35;MP=8.7e-01;GP=1.3e-01;TG=TT/CTTTT;TP=7.6e-01;SG=CT/CTTTT;SP=1.1e-01;VD=NOC2L|CCDS3.1|downstream;VW=SAMD11|CCDS2.2|intronic	GT:AA:CA:GA:TA:PM	0/0:0:0:0:10:0.0e+00	0/1:0:5:1:19:2.0e-01
1	915246	595026982	T	G	.	PH;DP	DP=95;MP=1.0e+00;GP=9.1e-06;TG=TT/GTTTT;TP=1.0e+00;SG=TT/GGTTT;SP=4.7e-03;CA;VD=PLEKHN1|CCDS4.1|downstream;VW=C1orf170|ENST00000433179|r.882a>c|c.882A>C|p.T294T	GT:AA:CA:GA:TA:PM	0/0:0:1:0:24:0.0e+00	0/1:0:0:15:55:2.1e-01
1	915369	595026983	T	G	.	PH;DP;UM;MN	DP=149;MP=9.4e-01;GP=5.1e-02;TG=TT/GTTTT;TP=9.4e-01;SG=GT/GTTTT;SP=5.1e-02;CA;VD=PLEKHN1|CCDS4.1|downstream;VW=C1orf170|ENST00000433179|r.759a>c|c.759A>C|p.T253T	GT:AA:CA:GA:TA:PM	0/0:0:0:1:18:5.3e-02	0/1:0:0:12:118:9.2e-02
1	915459	595026984	T	G	.	PH	DP=99;MP=9.3e-01;GP=7.2e-02;TG=TT/GTTTT;TP=9.3e-01;SG=GT/GTTTT;SP=7.2e-02;CA;VD=PLEKHN1|CCDS4.1|downstream;VW=C1orf170|ENST00000433179|r.669a>c|c.669A>C|p.T223T	GT:AA:CA:GA:TA:PM	0/0:0:0:0:11:0.0e+00	0/1:0:0:9:79:1.0e-01
1	981307	595026985	A	C	.	PH;DP	DP=59;MP=1.0e+00;GP=3.7e-04;TG=AA/AAAAC;TP=8.4e-01;SG=AA/AAACC;SP=1.6e-01;VD=AGRN|CCDS30551.1|intronic;VW=AGRN|CCDS30551.1|intronic	GT:AA:CA:GA:TA:PM	0/0:19:0:0:0:0.0e+00	0/1:30:10:0:0:2.5e-01
1	1203428	595026986	T	C	.	PH;DP	DP=213;MP=9.8e-01;GP=3.4e-17;TG=TT/CTTTT;TP=9.8e-01;SG=TT/TTTTT;SP=2.1e-02;VD=UBE2J2|CCDS16.1|intronic;VW=UBE2J2|CCDS16.1|intronic	GT:AA:CA:GA:TA:PM	0/0:0:0:0:64:0.0e+00	0/1:0:15:0:134:1.0e-01
1	1225535	595026987	T	C	.	SR	DP=24;MP=9.1e-01;GP=9.7e-03;TG=TT/CCTTT;TP=4.4e-01;SG=TT/CTTTT;SP=3.7e-01;VD=ACAP3|CCDS19.2|downstream;VW=SCNN1D|CCDS18.1|intronic	GT:AA:CA:GA:TA:PM	0/0:0:0:0:14:0.0e+00	0/1:0:3:0:7:3.0e-01
1	1249680	595026988	C	T	.	PASS	DP=29;MP=9.8e-01;GP=2.0e-02;TG=CC/CCCTT;TP=5.6e-01;SG=CC/CCCCT;SP=3.6e-01;CA;VD=CPSF3L|CCDS21.1|r.850+1g>a|c.767+1G>A|p.?;VW=CPSF3L|CCDS21.1|r.850+1g>a|c.767+1G>A|p.?	GT:AA:CA:GA:TA:PM	0/0:0:13:0:0:0.0e+00	0/1:0:11:0:5:3.1e-01
1	1264136	595026989	A	T	.	PASS	DP=63;MP=1.0e+00;GP=6.3e-08;TG=AA/AAAAT;TP=8.6e-01;SG=AA/AAATT;SP=1.4e-01;SNP;VD=GLTPD1|CCDS30555.1|r.2049a>u|c.?|p.?;VW=GLTPD1|CCDS30555.1|r.2049a>u|c.?|p.?	GT:AA:CA:GA:TA:PM	0/0:32:0:0:0:0.0e+00	0/1:24:0:0:7:2.3e-01
1	1268403	595026990	G	A	.	PASS	DP=83;MP=1.0e+00;GP=1.5e-12;TG=GG/AAAGG;TP=9.3e-01;SG=GG/AAGGG;SP=3.8e-02;CA;VD=TAS1R3|CCDS30556.1|r.1410g>a|c.1378G>A|p.V460M;VW=TAS1R3|CCDS30556.1|r.1410g>a|c.1378G>A|p.V460M	GT:AA:CA:GA:TA:PM	0/0:0:0:48:0:0.0e+00	0/1:21:0:14:0:6.0e-01
1	1273314	595026991	G	A	.	SR	DP=15;MP=8.6e-01;GP=1.3e-01;TG=GG/AAAGG;TP=3.6e-01;SG=GG/AAGGG;SP=2.3e-01;VD=TAS1R3|CCDS30556.1|downstream;VW=DVL1L1|CCDS22.1|intronic	GT:AA:CA:GA:TA:PM	0/0:0:0:10:0:0.0e+00	0/1:3:0:2:0:6.0e-01
1	1275688	595026992	G	A	.	PASS	DP=105;MP=1.0e+00;GP=7.2e-15;TG=GG/AAAGG;TP=9.6e-01;SG=GG/AAGGG;SP=3.5e-02;CA;VD=DVL1L1|CCDS22.1|r.755c>u|c.708C>T|p.S236S;VW=DVL1L1|CCDS22.1|r.755c>u|c.708C>T|p.S236S	GT:AA:CA:GA:TA:PM	0/0:0:0:56:0:0.0e+00	0/1:28:0:21:0:5.7e-01
1	1374508	595026993	G	A	.	PASS	DP=40;MP=1.0e+00;GP=9.8e-05;TG=GG/AAGGG;TP=5.4e-01;SG=GG/AAAGG;SP=4.4e-01;CA;VD=VWA1|CCDS27.1|r.757g>a|c.679G>A|p.G227S;VW=VWA1|CCDS27.1|r.757g>a|c.679G>A|p.G227S	GT:AA:CA:GA:TA:PM	0/0:0:0:21:0:0.0e+00	0/1:9:0:10:0:4.7e-01
1	1390967	595026994	C	A	.	PASS	DP=51;MP=1.0e+00;GP=2.7e-03;TG=CC/AACCC;TP=8.0e-01;SG=CC/ACCCC;SP=1.9e-01;VD=ATAD3C|CCDS44039.1|intronic;VW=ATAD3C|CCDS44039.1|intronic	GT:AA:CA:GA:TA:PM	0/0:0:16:0:0:0.0e+00	0/1:11:23:1:0:3.1e-01
