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Ref_tutorial.recode.vcf
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Ref_tutorial.recode.vcf
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##fileformat=VCFv4.2
"##fileDate=Dec 6, 2017 12:24:13 PM"
##source=MELTv2.1.4
##reference=human_g1k_v37_decoy_phiX.fasta
"##ALT=<ID=CN0,Description=""Copy number allele: 0 copies"">"
"##contig=<ID=1,length=249250621>"
"##contig=<ID=10,length=135534747>"
"##contig=<ID=11,length=135006516>"
"##contig=<ID=12,length=133851895>"
"##contig=<ID=13,length=115169878>"
"##contig=<ID=14,length=107349540>"
"##contig=<ID=15,length=102531392>"
"##contig=<ID=16,length=90354753>"
"##contig=<ID=17,length=81195210>"
"##contig=<ID=18,length=78077248>"
"##contig=<ID=19,length=59128983>"
"##contig=<ID=2,length=243199373>"
"##contig=<ID=20,length=63025520>"
"##contig=<ID=21,length=48129895>"
"##contig=<ID=22,length=51304566>"
"##contig=<ID=3,length=198022430>"
"##contig=<ID=4,length=191154276>"
"##contig=<ID=5,length=180915260>"
"##contig=<ID=6,length=171115067>"
"##contig=<ID=7,length=159138663>"
"##contig=<ID=8,length=146364022>"
"##contig=<ID=9,length=141213431>"
"##contig=<ID=X,length=155270560>"
"##contig=<ID=Y,length=59373566>"
"##FORMAT=<ID=GT,Number=1,Type=String,Description=""Genotype"">"
"##FORMAT=<ID=GL,Number=3,Type=Float,Description=""Genotype likelihood"">"
"##INFO=<ID=SVTYPE,Number=1,Type=String,Description=""Original element type according to repeatmasker"">"
"##INFO=<ID=END,Number=1,Type=Integer,Description=""End coordinate of this variant"">##INFO=<ID=SVLEN,Number=1,Type=Integer,Description=""Difference in length between REF and ALT alleles; If there is only 5' OR 3' support for this call , will be -1"">"
"##INFO=<ID=ADJLEFT,Number=1,Type=Integer,Description=""Left bound of deletion if different from repeatmasker, else 0"">"
"##INFO=<ID=ADJRIGHT,Number=1,Type=Integer,Description=""Right bound of deletion if different from repeatmasker, else 0"">"
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12348 NA12413 NA12716
chr10 61983855 . T <CN:0> . . SVTYPE=AluYb8;END=63743793;SVLEN=165;ADJLEFT=63743628;ADJRIGHT=63743793 GT:GL "0/0:-0.6,-6.02,-97" "0/0:-0,-4.82,-79.8" "0/0:-0.6,-2.41,-36.6"
chr11 14326764 . G <CN:0> . . SVTYPE=AluYa5;END=14348627;SVLEN=302;ADJLEFT=14348325;ADJRIGHT=14348627 GT:GL "0/1:-29,-6.62,-72.01" "0/1:-46.4,-7.83,-60.01" "0/1:-29,-9.63,-132.01"
chr2 222616971 . T <CN:0> . . SVTYPE=AluYb8;END=223481980;SVLEN=274;ADJLEFT=223481706;ADJRIGHT=0 GT:GL "0/1:-29,-6.02,-60.01" "0/1:-44,-11.44,-132.03" "0/1:-29,-4.21,-24.01"
chr3 49456843 . T <CN:0> . . SVTYPE=AluYa5;END=49494606;SVLEN=316;ADJLEFT=49494290;ADJRIGHT=49494606 GT:GL "0/1:-17.4,-3.01,-24" "1/1:-40.6,-4.21,-0.01" "0/1:-23.2,-3.61,-24"
chr8 115475989 . T <CN:0> . . SVTYPE=AluYa5;END=116488546;SVLEN=305;ADJLEFT=116488241;ADJRIGHT=116488546 GT:GL "0/0:-0.6,-3.01,-42.4" "0/1:-23.2,-5.42,-44.4" "0/0:-0,-4.21,-72.4"