##reference=file://\Genomes\Homo_sapiens\UCSC\hg19\Sequence\WholeGenomeFASTA\genome.fa
##gvcftools_version="0.12.1"
##gvcftools_cmdline="C:\Illumina\MiSeq Reporter\Workflows\PcrAmpliconWorker\gatk_to_gvcf.exe --no-default-filters --min-qd 0.0000 --min-gqx 10.0000 --min-mq 0.0000"
##source=GATK 1.6
##source_20170411.1=vcf-merge(v0.1.14-12-gcdb80b8) CK-F27NA_S42.genome.vcf.gz CV-F08AN_S49.genome.vcf.gz F06NA-JB_S14.genome.vcf.gz F11NA_S17.genome.vcf.gz F12AN-SS-Repeat_S2.genome.vcf.gz F12AN-SS_S1.genome.vcf.gz F13NA_S4.genome.vcf.gz F14AN_S5.genome.vcf.gz F15AN-BP_S8.genome.vcf.gz F17NA_S29.genome.vcf.gz F19NA_S6.genome.vcf.gz F20AN-LP_S3.genome.vcf.gz F23NA_S45.genome.vcf.gz F25NA_S36.genome.vcf.gz F32AN_S23.genome.vcf.gz F33NA_S44.genome.vcf.gz F38AN_S43.genome.vcf.gz F50an_S48.genome.vcf.gz F52AN_S30.genome.vcf.gz F54AN_S33.genome.vcf.gz F56AN_S32.genome.vcf.gz F66AN_S51.genome.vcf.gz FA2AN_S37.genome.vcf.gz FO1AN-Repeat_S38.genome.vcf.gz FO1AN_S9.genome.vcf.gz FO3AN-EMT_S10.genome.vcf.gz FO5NA-JS_S13.genome.vcf.gz Furan-TC_S21.genome.vcf.gz IG-M24AN_S27.genome.vcf.gz IO-M43NA_S50.genome.vcf.gz JM-MO4AN_S12.genome.vcf.gz JW-FS0AN_S24.genome.vcf.gz LC-F29NA_S35.genome.vcf.gz M09NA_S31.genome.vcf.gz M10AN_S7.genome.vcf.gz M21NA_S39.genome.vcf.gz M28AN-RL_S40.genome.vcf.gz M39NA_S20.genome.vcf.gz M47NA_S22.genome.vcf.gz M62AN_S53.genome.vcf.gz M68AN_S52.genome.vcf.gz MMI-F40AN-BIP4-FM_S34.genome.vcf.gz MN22NAD_S41.genome.vcf.gz MO2AN-EG_S11.genome.vcf.gz MO4AN-JM_S15.genome.vcf.gz MO7AN-Repeat_S18.genome.vcf.gz MO7AN_S16.genome.vcf.gz RF-F46AN_S28.genome.vcf.gz RT-F30AN_S46.genome.vcf.gz f44AN_S19.genome.vcf.gz f47NA_S47.genome.vcf.gz f49na_S26.genome.vcf.gz f51na_S25.genome.vcf.gz
##sourceFiles_20170411.1=0:CK-F27NA_S42.genome.vcf.gz,1:CV-F08AN_S49.genome.vcf.gz,2:F06NA-JB_S14.genome.vcf.gz,3:F11NA_S17.genome.vcf.gz,4:F12AN-SS-Repeat_S2.genome.vcf.gz,5:F12AN-SS_S1.genome.vcf.gz,6:F13NA_S4.genome.vcf.gz,7:F14AN_S5.genome.vcf.gz,8:F15AN-BP_S8.genome.vcf.gz,9:F17NA_S29.genome.vcf.gz,10:F19NA_S6.genome.vcf.gz,11:F20AN-LP_S3.genome.vcf.gz,12:F23NA_S45.genome.vcf.gz,13:F25NA_S36.genome.vcf.gz,14:F32AN_S23.genome.vcf.gz,15:F33NA_S44.genome.vcf.gz,16:F38AN_S43.genome.vcf.gz,17:F50an_S48.genome.vcf.gz,18:F52AN_S30.genome.vcf.gz,19:F54AN_S33.genome.vcf.gz,20:F56AN_S32.genome.vcf.gz,21:F66AN_S51.genome.vcf.gz,22:FA2AN_S37.genome.vcf.gz,23:FO1AN-Repeat_S38.genome.vcf.gz,24:FO1AN_S9.genome.vcf.gz,25:FO3AN-EMT_S10.genome.vcf.gz,26:FO5NA-JS_S13.genome.vcf.gz,27:Furan-TC_S21.genome.vcf.gz,28:IG-M24AN_S27.genome.vcf.gz,29:IO-M43NA_S50.genome.vcf.gz,30:JM-MO4AN_S12.genome.vcf.gz,31:JW-FS0AN_S24.genome.vcf.gz,32:LC-F29NA_S35.genome.vcf.gz,33:M09NA_S31.genome.vcf.gz,34:M10AN_S7.genome.vcf.gz,35:M21NA_S39.genome.vcf.gz,36:M28AN-RL_S40.genome.vcf.gz,37:M39NA_S20.genome.vcf.gz,38:M47NA_S22.genome.vcf.gz,39:M62AN_S53.genome.vcf.gz,40:M68AN_S52.genome.vcf.gz,41:MMI-F40AN-BIP4-FM_S34.genome.vcf.gz,42:MN22NAD_S41.genome.vcf.gz,43:MO2AN-EG_S11.genome.vcf.gz,44:MO4AN-JM_S15.genome.vcf.gz,45:MO7AN-Repeat_S18.genome.vcf.gz,46:MO7AN_S16.genome.vcf.gz,47:RF-F46AN_S28.genome.vcf.gz,48:RT-F30AN_S46.genome.vcf.gz,49:f44AN_S19.genome.vcf.gz,50:f47NA_S47.genome.vcf.gz,51:f49na_S26.genome.vcf.gz,52:f51na_S25.genome.vcf.gz
##INFO=<ID=SF,Number=.,Type=String,Description="Source File (index to sourceFiles, f when filtered)">
##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	CK-F27NA	CV-F08AN	F06NA-JB	F11NA	F12AN-SS-Repeat	F12AN-SS	F13NA	F14AN	F15AN-BP	F17NA	F19NA	F20AN-LP	F23NA	F25NA	F32AN	F33NA	F38AN	F50an	F52AN	F54AN	F56AN	F66AN	FA2AN	FO1AN-Repeat	FO1AN	FO3AN-EMT	FO5NA-JS	Furan-TC	IG-M24AN	IO-M43NA	JM-MO4AN	JW-FS0AN	LC-F29NA	M09NA	M10AN	M21NA	M28AN-RL	M39NA	M47NA	M62AN	M68AN	MMI-F40AN-BIP4-FM	MN22NAD	MO2AN-EG	MO4AN-JM	MO7AN-Repeat	MO7AN	RF-F46AN	RT-F30AN	f44AN	f47NA	f49na	f51na
chr22	19951229	.	G	.	.	PASS	AC=0;AN=106;BLOCKAVG_min30p3a;END=19951270;SF=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52	GT:MQ:DP:GQX	0/0:60:3726:99	0/0:60:3233:99	0/0:60:4124:99	0/0:60:4357:99	0/0:60:3603:99	0/0:60:4413:99	0/0:60:4296:99	0/0:60:4988:99	0/0:60:4924:99	0/0:60:4125:99	0/0:60:4262:99	0/0:60:4954:99	0/0:60:3528:99	0/0:60:3502:99	0/0:60:4464:99	0/0:60:4237:99	0/0:60:3835:99	0/0:60:3380:99	0/0:60:4867:99	0/0:60:4183:99	0/0:60:3930:99	0/0:60:3877:99	0/0:60:3899:99	0/0:60:3900:99	0/0:60:4391:99	0/0:60:1775:99	0/0:60:3932:99	0/0:60:4996:99	0/0:60:4701:99	0/0:60:2609:99	0/0:60:4996:99	0/0:60:2390:99	0/0:60:4440:99	0/0:60:4481:99	0/0:60:4994:99	0/0:60:4996:99	0/0:60:3897:99	0/0:60:4857:99	0/0:60:4993:99	0/0:60:3611:99	0/0:60:3513:99	0/0:60:3358:99	0/0:60:4986:99	0/0:60:4994:99	0/0:60:4994:99	0/0:60:4550:99	0/0:60:3775:99	0/0:60:3546:99	0/0:60:4996:99	0/0:60:4994:99	0/0:60:3549:99	0/0:60:4149:99	0/0:60:3724:99
chr22	19951237	rs8192488	C	T	43236.76	PASS	AC=1;AN=2;BaseQRankSum=18.671;DP=4238;Dels=0.00;EXON;FC=Synonymous_A146A,Synonymous_A146A,Synonymous_A146A,Synonymous_A96A;FS=0.335;GI=COMT,COMT,COMT,COMT;HRun=0;HaplotypeScore=312.5883;MQ0=0;MQ=60;MQRankSum=0.292;QD=10.20;ReadPosRankSum=-0.150;SB=-37360.60;SF=15;TI=NM_000754,NM_001135161,NM_001135162,NM_007310	GT:MQ:GQ:DP:VF:GQX:PL:AD	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0/1:60:99:4238:0.523:99:43237,0,38686:2019,2218	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
chr22	19951238	.	G	.	.	PASS	AC=0;AN=2;BLOCKAVG_min30p3a;END=19951297;SF=15	GT:MQ:DP:GQX	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0/0:60:4234:99	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
chr22	19951271	rs4680	G	A	63681.55	PASS	AC=48;AN=70;BaseQRankSum=16.837;DP=146789;DS;Dels=0.00;EXON;FC=Missense_V158M,Missense_V158M,Missense_V158M,Missense_V108M;FS=0.881;GI=COMT,COMT,COMT,COMT;HRun=0;HaplotypeScore=343.3303;MQ0=0;MQ=60;MQRankSum=-1.344;QD=10.50;ReadPosRankSum=0.610;SB=-34171.72;SF=0,1,2,6,8,9,10,11,12,13,14,16,17,18,19,20,21,22,23,24,26,27,28,33,35,36,37,38,40,41,43,47,49,51,52;TI=NM_000754,NM_001135161,NM_001135162,NM_007310	GT:MQ:GQ:DP:VF:GQX:PL:AD	0/1:60:99:3736:0.537:99:39235,0,32898:1729,2003	0/1:60:99:3241:0.564:99:36021,0,26558:1413,1827	0/1:60:99:4132:0.536:99:43428,0,36551:1913,2213	.	.	.	0/1:60:99:4301:0.536:99:45021,0,37877:1995,2304	.	0/1:60:99:4936:0.538:99:51973,0,43205:2278,2656	0/1:60:99:4139:0.542:99:44126,0,36076:1896,2240	0/1:60:99:4277:0.500:99:41428,0,41199:2137,2137	0/1:60:99:4964:0.546:99:53190,0,42619:2253,2707	0/1:60:99:3536:0.558:99:38803,0,29517:1561,1973	0/1:60:99:3506:0.533:99:36489,0,31360:1638,1866	1/1:60:99:4470:0.994:99:98940,6189,0:28,4440	.	0/1:60:99:3839:0.553:99:41740,0,32299:1714,2123	0/1:60:99:3382:0.583:99:38837,0,26322:1409,1966	0/1:60:99:4875:0.507:99:47878,0,46071:2403,2469	1/1:60:99:4189:0.992:99:92550,5693,0:32,4155	1/1:60:99:3942:0.995:99:87222,5542,0:18,3918	1/1:60:99:3885:0.995:99:86010,5505,0:19,3861	0/1:60:99:3905:0.552:99:42439,0,33124:1748,2156	1/1:60:99:3908:0.994:99:86449,5375,0:25,3880	1/1:60:99:4397:0.996:99:97665,6282,0:17,4377	.	1/1:60:99:3938:0.996:99:87375,5627,0:17,3915	0/1:60:99:5000:0.583:99:63049,0,42538:2085,2914	0/1:60:99:4710:0.585:99:54499,0,36234:1950,2753	.	.	.	.	1/1:60:99:4490:0.995:99:99493,6280,0:23,4465	.	0/1:60:99:5000:0.505:99:61828,0,60347:2473,2521	1/1:60:99:3904:0.995:99:86402,5526,0:20,3879	1/1:60:99:4867:0.996:99:107774,6857,0:21,4842	1/1:60:99:5000:0.994:99:121597,7818,0:30,4962	.	1/1:60:99:3520:0.996:99:78115,5002,0:14,3505	0/1:60:99:3363:0.543:99:35846,0,28861:1535,1826	.	0/1:60:99:4999:0.561:99:57929,0,43433:2192,2804	.	.	.	1/1:60:99:3552:0.993:99:78065,4770,0:26,3524	.	0/1:60:99:4999:0.513:99:59394,0,55175:2435,2560	.	0/1:60:99:4155:0.568:99:46391,0,33767:1794,2357	0/1:60:99:3729:0.567:99:41654,0,30275:1613,2113
chr22	19951272	.	T	.	.	PASS	AC=0;AN=70;BLOCKAVG_min30p3a;END=19951297;SF=0,1,2,6,8,9,10,11,12,13,14,16,17,18,19,20,21,22,23,24,26,27,28,33,35,36,37,38,40,41,43,47,49,51,52	GT:MQ:DP:GQX	0/0:60:3734:99	0/0:60:3239:99	0/0:60:4128:99	.	.	.	0/0:60:4299:99	.	0/0:60:4934:99	0/0:60:4137:99	0/0:60:4275:99	0/0:60:4961:99	0/0:60:3535:99	0/0:60:3502:99	0/0:60:4463:99	.	0/0:60:3835:99	0/0:60:3381:99	0/0:60:4875:99	0/0:60:4183:99	0/0:60:3940:99	0/0:60:3881:99	0/0:60:3901:99	0/0:60:3904:99	0/0:60:4397:99	.	0/0:60:3934:99	0/0:60:4998:99	0/0:60:4704:99	.	.	.	.	0/0:60:4488:99	.	0/0:60:4997:99	0/0:60:3902:99	0/0:60:4865:99	0/0:60:4998:99	.	0/0:60:3518:99	0/0:60:3361:99	.	0/0:60:4996:99	.	.	.	0/0:60:3550:99	.	0/0:60:4995:99	.	0/0:60:4153:99	0/0:60:3727:99