##fileformat=VCFv4.1
##fileDate=20150126
##reference=hs37d5
##phasing=partial
##FILTER=<ID=INDEL_SPECIFIC_FILTERS,Description="QD < 2.0 || ReadPosRankSum < -20.0 || InbreedingCoeff < -0.8 || FS > 200.0">
##FILTER=<ID=LowQual,Description="Low quality">
##FILTER=<ID=VQSRTrancheSNP99.00to99.90,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -6.6778 <= x < -0.6832">
##FILTER=<ID=VQSRTrancheSNP99.90to100.00+,Description="Truth sensitivity tranche level for SNP model at VQS Lod < -36469.5723">
##INFO=<ID=TRAILING,Number=.,Type=Integer,Description="This line contains trailing spaces for testing purposes">               
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=GQ,Number=1,Type=Integer,EmptyWithSpace= ,Description="Genotype Quality">
##FORMAT=<ID=GATK,Number=1, Type  =   String    ,     Description="Genotype as called by GATK. Always a diploid call. All other genotype stats based on this genotype.">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype after Personalis post-processing to match detected chromosome counts.">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001
1	12065947	PTV001	C	T,A	29	PASS	.	GT:GATK:AD:DP:GQ	0/1:0/1:3,2:5:19
1	109817590	PTV002	G	T	77	PASS	.	GT:GATK:AD:DP:GQ	0/1:0/1:3,2:5:20
1	153791300	PTV003	CTG	C	81	PASS	.	GT:GATK:AD:DP:GQ	0/1:0/1:3,2:5:21
1	156104666	PTV004	TTGAGAGCCGGCTGGCGGAT	TCC	30	PASS	.	GT:GATK:AD:DP:GQ	0/1:0/1:3,2:5:22
1	156108541	PTV005	G	GG	31	PASS	.	GT:GATK:AD:DP:GQ	0/1:0/1:3,2:5:23
1	161279695	PTV006	T	C,A	32	PASS	.	GT:GATK:AD:DP:GQ	0/1:0/1:3,2:5:24
1	169519049	PTV007	T	.	35	PASS	.	GT:GATK:AD:DP:GQ	0/1:0/1:3,2:5:24
1	226125468	PTV097	G	A	99	PASS	.	GT:GATK:AD:DP:GQ	0/1:0/1:3,2:5:109
16	2103394	PTV056	C	T	68	PASS	.	GT:GATK:AD:DP:GQ	0/1:0/1:3,2:5:72
4	31789170	PTV021	G	.	77	PASS	.	GT:GATK:AD:DP:GQ	0/1:0/1:3,2:5:38