##fileformat=VCFv4.1
##fileDate=20180426
##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>
##contig=<ID=5,length=180915260,assembly=null,md5=0740173db9ffd264d728f32784845cd7,species=null>
##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>
##contig=<ID=9,length=141213431,assembly=null,md5=3e273117f15e0a400f01055d9f393768,species=null>
##contig=<ID=10,length=135534747,assembly=null,md5=988c28e000e84c26d552359af1ea2e1d,species=null>
##contig=<ID=11,length=135006516,assembly=null,md5=98c59049a2df285c76ffb1c6db8f8b96,species=null>
##contig=<ID=12,length=133851895,assembly=null,md5=51851ac0e1a115847ad36449b0015864,species=null>
##contig=<ID=13,length=115169878,assembly=null,md5=283f8d7892baa81b510a015719ca7b0b,species=null>
##contig=<ID=14,length=107349540,assembly=null,md5=98f3cae32b2a2e9524bc19813927542e,species=null>
##contig=<ID=15,length=102531392,assembly=null,md5=e5645a794a8238215b2cd77acb95a078,species=null>
##contig=<ID=16,length=90354753,assembly=null,md5=fc9b1a7b42b97a864f56b348b06095e6,species=null>
##contig=<ID=17,length=81195210,assembly=null,md5=351f64d4f4f9ddd45b35336ad97aa6de,species=null>
##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=none
##phasing=none
##geneAnno=none
##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=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=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
##FORMAT=<ID=CM,Number=1,Type=Integer,Description="Number of Unconverted Cytosines in this position(filtered by minConv)">
##FORMAT=<ID=GP,Number=G,Type=Integer,Description="Normalized, Phred-scaled posteriors for genotypes as defined in the VCF specification">
##INFO=<ID=HQ,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##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=SS,Number=1,Type=Integer,Description="Somatic status of the variant. 1) wildtype; 2) germline, somatic; 3) LOH; 4) post-transcriptional modification; 5) unknown">
##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
##BisSNP-1.0.0 Program Args= -R /home/Shared_taupo/data/annotation/Human/GRCH37/Bisulfite_Genome.release91/GRCh37.91.fa -T BisulfiteGenotyper -I /home/Shared/steph/CRC.bismark.bams/NORM1_pe.dedupl_s.bam -D common_all_20170710.vcf -vfn1 NORM1/NORM1.het.snp.raw.vcf -L /home/Shared/steph/130912_HG19_CpGiant_4M_EPI.bed -out_modes EMIT_HET_SNPS_ONLY -nt 20
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth, not filtered by mapping quality and base quality score criteria yet">
##INFO=<ID=CS,Number=1,Type=Character,Description="Strand of cytosine relative to reference genome. Does not apply to non-cytosine positions">
##FORMAT=<ID=CP,Number=1,Type=String,Description="Best Cytosine Context">
##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=BQ,Number=.,Type=Float,Description="Average base quality for reads supporting alleles. For each allele, in the same order as listed">
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
##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">
##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	377.42	PASS	CS=+;DB;DP=61;MQ0=0;NS=1;REF=C,CH;SB=-232.6132	GT:BQ:BRC6:CM:CP:CU:DP:DP4:GP:GQ:SS	0/1:36.1,36.3:0,26,0,21,14,0:.:.:.:.:0,21,26,14:377,0,748:99:5
19	267213	rs11668555	C	T	121.94	PASS	CS=+;DB;DP=14;MQ0=0;NS=1;REF=C,CH;SB=-0.2081	GT:BQ:BRC6:CM:CP:CU:DP:DP4:GP:GQ:SS	0/1:35.8,34.8:0,3,0,5,4,0:.:.:.:.:0,5,5,4:122,0,179:99:5
19	267474	rs1020383	A	G	240.91	PASS	DB;DP=18;MQ0=0;NS=1;SB=-221.5035	GT:BQ:BRC6:CM:CP:CU:DP:DP4:GP:GQ:SS	0/1:33.5,37.5:0,0,18,0,0,0:.:.:.:.:8,0,10,0:344,0,241:99:5
19	267614	rs17603472	A	C	903.93	PASS	DB;DP=67;MQ0=0;NS=1;SB=-633.7306	GT:BQ:BRC6:CM:CP:CU:DP:DP4:GP:GQ:SS	0/1:35.7,35.6:0,20,28,11,0,8:.:.:.:.:28,8,0,11:904,0,1234:99:5
19	281360	rs7815	C	T	362.03	PASS	CS=+;DB;DP=73;MQ0=0;NS=1;REF=C,CH;SB=-184.2620	GT:BQ:BRC6:CM:CP:CU:DP:DP4:GP:GQ:SS	0/1:35.8,36.6:0,46,0,13,12,0:.:.:.:.:0,13,48,12:362,0,431:99:5
19	289877	rs12977857	G	A	211.88	PASS	CS=-;DB;DP=30;MQ0=0;NS=1;REF=C,CG;SB=-185.1466	GT:BQ:BRC6:CM:CP:CU:DP:DP4:GP:GQ:SS	0/1:36.4,35.4:0,0,23,0,0,5:.:.:.:.:15,1,8,6:212,0,580:99:5
19	290642	rs8102122	A	T	85.23	PASS	DB;DP=9;MQ0=0;NS=1;SB=-145.6981	GT:BQ:BRC6:CM:CP:CU:DP:DP4:GP:GQ:SS	0/1:36.3,38.0:0,6,1,0,0,2:.:.:.:.:1,2,6,0:184,0,85:85:5
19	292082	rs3813154	C	T	611.59	PASS	CS=+;DB;DP=69;MQ0=0;NS=1;REF=C,CH;SB=-281.2497	GT:BQ:BRC6:CM:CP:CU:DP:DP4:GP:GQ:SS	0/1:37.0,35.5:0,25,0,23,21,0:.:.:.:.:0,23,25,21:612,0,828:99:5
19	292549	rs10409897	C	A	792.21	PASS	CS=+;DB;DP=48;MQ0=0;NS=1;REF=C,CH;SB=-539.7541	GT:BQ:BRC6:CM:CP:CU:DP:DP4:GP:GQ:SS	0/1:37.3,37.7:0,9,8,14,0,17:.:.:.:.:0,14,8,17:815,0,792:99:5
19	292583	rs895345	A	G	183.31	PASS	DB;DP=28;MQ0=0;NS=1;SB=-59.9827	GT:BQ:BRC6:CM:CP:CU:DP:DP4:GP:GQ:SS	0/1:35.7,36.3:0,0,9,0,0,19:.:.:.:.:6,19,3,0:243,0,183:99:5
