1##fileformat=VCFv4.1 2##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location"> 3##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> 4##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> 5##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> 6##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> 7##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block"> 8##FORMAT=<ID=MIN_GQ,Number=1,Type=Integer,Description="Minimum GQ observed within the GVCF block"> 9##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> 10##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias."> 11##GVCFBlock=minGQ=0(inclusive),maxGQ=5(exclusive) 12##INFO=<ID=BLOCK_SIZE,Number=1,Type=Integer,Description="Size of the homozygous reference GVCF block"> 13##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities"> 14##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> 15##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval"> 16##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes"> 17##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality"> 18##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads"> 19##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities"> 20##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias"> 21##contig=<ID=chr20,length=64444167,assembly=Homo_sapiens_assembly38.fasta> 22##source=SelectVariants 23#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA1 24chr20 69485 . G <NON_REF> . . BLOCK_SIZE=20;END=69510 GT:DP:GQ:MIN_DP:MIN_GQ:PL 0/0:94:99:82:99:0,120,1800 25chr20 69511 . A G,<NON_REF> 2253.77 . BaseQRankSum=1.169;DP=82;MQ=31.05;MQ0=0;MQRankSum=-0.866;ReadPosRankSum=1.689 GT:AD:DP:GQ:PL:SB 1/1:1,79,0:80:99:2284,207,0,2287,237,2316:0,1,46,33 26chr20 69512 . A <NON_REF> . . BLOCK_SIZE=10;END=69521 GT:DP:GQ:MIN_DP:MIN_GQ:PL 0/0:96:99:82:99:0,120,1800 27chr20 69522 . A <NON_REF> . . BLOCK_SIZE=27;END=69548 GT:DP:GQ:MIN_DP:MIN_GQ:PL 0/0:95:0:95:0:0,0,0 28chr20 69549 . T <NON_REF> . . BLOCK_SIZE=86;END=69634 GT:DP:GQ:MIN_DP:MIN_GQ:PL 0/0:6:16:5:16:0,16,90 29chr20 69635 . A T,<NON_REF> 60.77 . BaseQRankSum=0.937;DP=7;MQ=34.15;MQ0=0;MQRankSum=1.300;ReadPosRankSum=1.754 GT:AD:DP:GQ:PL:SB 0/1:4,3,0:7:10:10,0,119,101,128,229:0,4,0,3 30chr20 69762 . A <NON_REF> . . BLOCK_SIZE=1;END=69762 GT:DP:GQ:MIN_DP:MIN_GQ:PL 0/0:7:18:7:18:0,18,270 31chr20 69763 . A <NON_REF> . . BLOCK_SIZE=4;END=69766 GT:DP:GQ:MIN_DP:MIN_GQ:PL 0/0:7:21:7:21:0,21,253 32chr20 69767 . A <NON_REF> . . BLOCK_SIZE=4;END=69770 GT:DP:GQ:MIN_DP:MIN_GQ:PL 0/0:7:12:7:12:0,12,180 33chr20 69771 . TAAAAA T,<NON_REF> 60.77 . BaseQRankSum=0.937;DP=7;MQ=34.15;MQ0=0;MQRankSum=1.300;ReadPosRankSum=1.754 GT:AD:DP:GQ:PL:SB 0/1:0,0,0:0:20:20,0,119,101,128,229:0,4,0,3 34chr20 69777 . G <NON_REF> . . BLOCK_SIZE=10;END=69783 GT:DP:GQ:MIN_DP:MIN_GQ:PL 0/0:7:0:3:0:0,0,0 35chr20 69785 . T G,<NON_REF> 2253.77 . BaseQRankSum=1.169;DP=82;MQ=31.05;MQ0=0;MQRankSum=-0.866;ReadPosRankSum=1.689 GT:DP:GQ:PL:SB 1/1:80:99:2284,207,0,2287,237,2316:0,1,46,33 36