##fileformat=VCFv4.1
##fileDate=20180220
##tcgaversion=1.1
##vcfProcessLog=<InputVCF=<>, InputVCFSource=<>, InputVCFVer=<1.1>, InputVCFParam=<> InputVCFgeneAnno=<>>
##reference=<ID=null,Source=file:/home/Shared_taupo/data/annotation/Human/GRCH37/Bisulfite_Genome.release91/GRCh37.91.fa>
##contig=<ID=1,length=249250621,assembly=null,md5=1b22b98cdeb4a9304cb5d48026a85128,species=null>
##contig=<ID=2,length=243199373,assembly=null,md5=a0d9851da00400dec1098a9255ac712e,species=null>
##contig=<ID=3,length=198022430,assembly=null,md5=641e4338fa8d52a5b781bd2a2c08d3c3,species=null>
##contig=<ID=4,length=191154276,assembly=null,md5=23dccd106897542ad87d2765d28a19a1,species=null>
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##contig=<ID=6,length=171115067,assembly=null,md5=1d3a93a248d92a729ee764823acbbc6b,species=null>
##contig=<ID=7,length=159138663,assembly=null,md5=618366e953d6aaad97dbe4777c29375e,species=null>
##contig=<ID=8,length=146364022,assembly=null,md5=96f514a9929e410c6651697bded59aec,species=null>
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##contig=<ID=13,length=115169878,assembly=null,md5=283f8d7892baa81b510a015719ca7b0b,species=null>
##contig=<ID=14,length=107349540,assembly=null,md5=98f3cae32b2a2e9524bc19813927542e,species=null>
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##contig=<ID=18,length=78077248,assembly=null,md5=b15d4b2d29dde9d3e4f93d1d0f2cbc9c,species=null>
##contig=<ID=19,length=59128983,assembly=null,md5=1aacd71f30db8e561810913e0b72636d,species=null>
##contig=<ID=20,length=63025520,assembly=null,md5=0dec9660ec1efaaf33281c0d5ea2560f,species=null>
##contig=<ID=21,length=48129895,assembly=null,md5=2979a6085bfe28e3ad6f552f361ed74d,species=null>
##contig=<ID=22,length=51304566,assembly=null,md5=a718acaa6135fdca8357d5bfe94211dd,species=null>
##contig=<ID=X,length=155270560,assembly=null,md5=7e0e2e580297b7764e31dbc80c2540dd,species=null>
##contig=<ID=Y,length=59373566,assembly=null,md5=1fa3474750af0948bdf97d5a0ee52e51,species=null>
##contig=<ID=MT,length=16569,assembly=null,md5=c68f52674c9fb33aef52dcf399755519,species=null>
##assembly=none
##center=USC Epigenome Center
##phasing=none
##geneAnno=none
##BisSNP-0.82.2 Program Args= -R /home/Shared_taupo/data/annotation/Human/GRCH37/Bisulfite_Genome.release91/GRCh37.91.fa -T BisulfiteGenotyper -I CRC1.recal.bam -D common_all_20170710.vcf -vfn1 CRC1.cpg.raw.vcf -vfn2 CRC1.snp.raw.vcf -L /home/Shared_sherborne/steph/130912_HG19_CpGiant_4M_EPI.bed -out_modes EMIT_HET_SNPS_ONLY -nt 10
##FORMAT=<ID=BQ,Number=.,Type=Float,Description="Average base quality for reads supporting alleles. For each allele, in the same order as listed">
##FORMAT=<ID=BRC6,Number=.,Type=Integer,Description="Bisulfite read counts(not filtered by minConv): 1) number of C in cytosine strand, 2) number of T in cytosine strand, 3) number of A/G/N in cytosine strand, 4) number of G in guanine strand, 5) number of A in guanine strand, 6) number of C/T/N in guanine strand.">
##FORMAT=<ID=CM,Number=1,Type=Integer,Description="Number of Unconverted Cytosines in this position(filtered by minConv)">
##FORMAT=<ID=CP,Number=1,Type=String,Description="Best Cytosine Context">
##FORMAT=<ID=CU,Number=1,Type=Integer,Description="Number of Converted Cytosines in this position(filtered by minConv)">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth, not filtered by mapping quality and base quality score criteria yet">
##FORMAT=<ID=DP4,Number=4,Type=Integer,Description="Reads supporting ALT, only keep good base. Number of 1) forward ref alleles; 2) reverse ref; 3) forward non-ref; 4) reverse non-ref alleles">
##FORMAT=<ID=GP,Number=G,Type=Integer,Description="Normalized, Phred-scaled posteriors for genotypes as defined in the VCF specification">
##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=SS,Number=1,Type=Integer,Description="Somatic status of the variant. 1) wildtype; 2) germline, somatic; 3) LOH; 4) post-transcriptional modification; 5) unknown">
##INFO=<ID=CS,Number=1,Type=Character,Description="Strand of cytosine relative to reference genome. Does not apply to non-cytosine positions">
##INFO=<ID=Context,Number=.,Type=String,Description="Cytosine Context. e.g. 'CG' means homozygous CG sites, while heterozygous CG sites will be output as IUPAC code">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth, not filtered by mapping quality and base quality score criteria yet">
##INFO=<ID=HQ,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
##INFO=<ID=REF,Number=.,Type=String,Description="Reference Cytosine Context. if all cytosine context found are in reference genome, REF=0; otherwise, e.g. it will be REF=CG for position not confidently called as CG or real context is CH.">
##INFO=<ID=SB,Number=1,Type=Float,Description="Strand Bias">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SAMPLE
19	267039	rs1020382	C	T	148.80	.	CS=+;Context=YH;DB;DP=68;MQ0=0;NS=1;REF=CH,C;SB=-1.5475	GT:BQ:BRC6:CM:CP:CU:DP:DP4:GP:GQ:SS	0/1:30.4,30.2:0,23,0,28,8,0:0:YH:23:68:0,28,23,8:149,0,879:99:5
19	267213	rs11668555	C	T	138.38	.	CS=+;Context=YH;DB;DP=35;MQ0=0;NS=1;REF=CH,C;SB=-18.7580	GT:BQ:BRC6:CM:CP:CU:DP:DP4:GP:GQ:SS	0/1:30.9,29.7:0,8,0,12,6,0:0:YH:8:35:0,12,8,6:138,0,377:99:5
19	267474	rs1020383	A	G	59.51	.	CS=-;Context=Y;DB;DP=10;MQ0=0;NS=1;SB=-18.7524	GT:BQ:BRC6:CM:CP:CU:DP:DP4:GP:GQ:SS	0/1:31.0,31.0:0,3,0,3,2,0:0:Y:3:10:2,3,3,0:81,0,60:59.51:5
19	267614	rs17603472	A	C	746.25	.	CS=+;Context=MH;DB;DP=72;MQ0=0;NS=1;SB=-470.5037	GT:BQ:BRC6:CM:CP:CU:DP:DP4:GP:GQ:SS	0/1:30.6,30.6:0,19,20,7,0,11:0:MH:19:72:20,11,0,7:746,0,927:99:5
19	281360	rs7815	C	T	473.04	.	CS=+;Context=YH;DB;DP=120;MQ0=2;NS=1;REF=CH,C;SB=-230.3667	GT:BQ:BRC6:CM:CP:CU:DP:DP4:GP:GQ:SS	0/1:30.4,30.2:0,32,0,37,19,0:0:YH:32:120:0,37,32,19:473,0,1136:99:5
19	289877	rs12977857	G	A	378.93	.	CS=-;Context=YG;DB;DP=53;MQ0=1;NS=1;REF=CG,C;SB=-324.4092	GT:BQ:BRC6:CM:CP:CU:DP:DP4:GP:GQ:SS	0/1:30.8,31.1:4,16,0,11,13,0:4:YG:16:53:11,4,13,16:379,0,417:99:5
19	290642	rs8102122	A	C	79.85	.	CS=+;Context=MH;DB;DP=29;MQ0=1;NS=1;SB=-13.5415	GT:BQ:BRC6:CM:CP:CU:DP:DP4:GP:GQ:SS	0/1:30.0,31.3:0,1,3,3,0,9:0:MH:1:29:3,9,0,3:80,0,372:79.85:5
19	292082	rs3813154	C	T	376.38	.	CS=+;Context=YH;DB;DP=53;MQ0=2;NS=1;REF=CH,C;SB=-121.6338	GT:BQ:BRC6:CM:CP:CU:DP:DP4:GP:GQ:SS	0/1:31.2,29.7:0,9,0,18,14,0:0:YH:9:53:0,18,9,14:376,0,554:99:5
19	292549	rs10409897	C	A	679.15	.	CS=+;Context=MH;DB;DP=61;MQ0=0;NS=1;REF=CH,C;SB=-612.0224	GT:BQ:BRC6:CM:CP:CU:DP:DP4:GP:GQ:SS	0/1:31.0,31.0:0,12,10,11,0,17:0:MH:12:61:0,11,9,17:765,0,679:99:5
19	292583	rs895345	A	G	204.45	.	CS=-;Context=YG;DB;DP=38;MQ0=0;NS=1;SB=-17.7478	GT:BQ:BRC6:CM:CP:CU:DP:DP4:GP:GQ:SS	0/1:31.0,31.0:3,13,0,6,7,0:3:YG:13:38:7,16,6,0:235,0,204:99:5
