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##fileformat=VCFv4.1
##fileDate=20141003
##reference=/shared/genomes/b37/full/human_g1k_v37.fasta
##INFO=<ID=TOOL,Number=1,Type=String,Description="Tool used to generate variant call">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
##INFO=<ID=STR,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format">
##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
##INFO=<ID=BKPTID,Number=.,Type=String,Description="ID of the assembled alternate allele in the assembly file">
##INFO=<ID=PARID,Number=1,Type=String,Description="ID of partner breakend">
##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends">
##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend">
##INFO=<ID=HOMLEN,Number=.,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">
##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints">
##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Somatic mutation">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
##INFO=<ID=SUP,Number=.,Type=Integer,Description="Number of pieces of evidence supporting the variant across all samples">
##INFO=<ID=PESUP,Number=.,Type=Integer,Description="Number of paired-end reads supporting the variant across all samples">
##INFO=<ID=SRSUP,Number=.,Type=Integer,Description="Number of split reads supporting the variant across all samples">
##INFO=<ID=EVTYPE,Number=.,Type=String,Description="Type of LUMPY evidence contributing to the variant call">
##INFO=<ID=PRIN,Number=0,Type=Flag,Description="Indicates variant as the principal variant in a BEDPE pair">
##ALT=<ID=DEL,Description="Deletion">
##ALT=<ID=DUP,Description="Duplication">
##ALT=<ID=INV,Description="Inversion">
##ALT=<ID=DUP:TANDEM,Description="Tandem duplication">
##ALT=<ID=INS,Description="Insertion of novel sequence">
##ALT=<ID=CNV,Description="Copy number variable region">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=SUP,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">
##FORMAT=<ID=PE,Number=1,Type=Integer,Description="Number of paired-end reads supporting the variant">
##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of split reads supporting the variant">
##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number genotype for imprecise events">
##FORMAT=<ID=CNQ,Number=1,Type=Float,Description="Copy number genotype quality for imprecise events">
##FORMAT=<ID=CNL,Number=.,Type=Float,Description="Copy number genotype likelihood form imprecise events">
##FORMAT=<ID=NQ,Number=1,Type=Integer,Description="Phred style probability score that the variant is novel">
##FORMAT=<ID=HAP,Number=1,Type=Integer,Description="Unique haplotype identifier">
##FORMAT=<ID=AHAP,Number=1,Type=Integer,Description="Unique identifier of ancestral haplotype">
##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count, with partial observations recorded fractionally">
##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally">
##FORMAT=<ID=SQ,Number=1,Type=Float,Description="Phred-scaled probability that this site is variant (non-reference in this sample">
##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
##VEP=v76 cache=/shared/external_bin/ensembl-tools-release-76/cache/homo_sapiens/76_GRCh37 db=.
##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence type as predicted by VEP. Format: Consequence|Codons|Amino_acids|Gene|SYMBOL|Feature|EXON|PolyPhen|SIFT|Protein_position|BIOTYPE">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT H_LS-E2-A14P-01A-31D-A19H-09 H_LS-E2-A14P-10A-01D-A19H-09
1 1866375 4 T <DEL> 920.58 . TOOL=LUMPY;SVTYPE=DEL;SVLEN=-619;END=1866994;STR=+-:49;IMPRECISE;CIPOS=-1,20;CIEND=0,0;EVENT=4;SUP=49;PESUP=49;SRSUP=0;EVTYPE=PE;PRIN;CSQ=intron_variant&feature_truncation|||ENSG00000142609|C1orf222|ENST00000493964||||-/867|protein_coding GT:SUP:PE:SR:GQ:DP:RO:AO:SQ:GL 1/1:26:26:0:0.00:28:2:26:221.74:-24,-8,-1 1/1:23:23:0:0.00:37:5:32:256.33:-27,-8,-1
3 178906030 1233_2 T [3:176909982[T 9.58 . TOOL=LUMPY;SVTYPE=BND;STR=--:26;IMPRECISE;CIPOS=-39,0;CIEND=-28,0;MATEID=1233_1;EVENT=1233;SUP=15;PESUP=15;SRSUP=0;EVTYPE=PE;CSQ=intron_variant|||ENSG00000121879|PIK3CA|ENST00000468036||||-/118|protein_coding,intron_variant|||ENSG00000121879|PIK3CA|ENST00000477735||||-/21|protein_coding,intron_variant|||ENSG00000121879|PIK3CA|ENST00000263967||||-/1068|protein_coding GT:SUP:PE:SR:GQ:DP:RO:AO:SQ:GL 0/1:15:15:0:0.51:124:94:29:9.58:-5,-4,-40 0/0:0:0:0:-0.00:90:90:0:.:-4,-20,-62
3 176909982 1233_1 G [3:178906030[G 9.58 . TOOL=LUMPY;SVTYPE=BND;STR=--:26;IMPRECISE;CIPOS=-28,0;CIEND=-39,0;MATEID=1233_2;EVENT=1233;SUP=15;PESUP=15;SRSUP=0;EVTYPE=PE;PRIN;CSQ=intron_variant|||ENSG00000177565|TBL1XR1|ENST00000443315||||-/81|protein_coding,intron_variant|||ENSG00000177565|TBL1XR1|ENST00000457928||||-/514|protein_coding,intron_variant|||ENSG00000177565|TBL1XR1|ENST00000431674||||-/96|protein_coding,intron_variant|||ENSG00000177565|TBL1XR1|ENST00000413084||||-/33|protein_coding,intron_variant|||ENSG00000177565|TBL1XR1|ENST00000427349||||-/62|protein_coding,intron_variant|||ENSG00000177565|TBL1XR1|ENST00000422066||||-/87|protein_coding,intron_variant|||ENSG00000177565|TBL1XR1|ENST00000430069||||-/514|protein_coding,intron_variant|||ENSG00000177565|TBL1XR1|ENST00000431421||||-/55|protein_coding,intron_variant|||ENSG00000177565|TBL1XR1|ENST00000352800||||-/142|protein_coding,intron_variant|||ENSG00000177565|TBL1XR1|ENST00000422442||||-/68|protein_coding,intron_variant|||ENSG00000177565|TBL1XR1|ENST00000424913||||-/73|protein_coding,intron_variant|||ENSG00000177565|TBL1XR1|ENST00000450267||||-/120|protein_coding,intron_variant|||ENSG00000177565|TBL1XR1|ENST00000428970||||-/76|protein_coding,intron_variant|||ENSG00000177565|TBL1XR1|ENST00000437738||||-/142|protein_coding GT:SUP:PE:SR:GQ:DP:RO:AO:SQ:GL 0/1:15:15:0:0.51:124:94:29:9.58:-5,-4,-40 0/0:0:0:0:-0.00:90:90:0:.:-4,-20,-62
18 64284796 9629_1 A A]X:6146702] 8.25 . TOOL=LUMPY;SVTYPE=BND;STR=++:11;IMPRECISE;CIPOS=-1,1;CIEND=0,0;MATEID=9629_2;EVENT=9629;SUP=9;PESUP=8;SRSUP=1;EVTYPE=PE,SR;PRIN;CSQ=intergenic_variant|||||||||| GT:SUP:PE:SR:GQ:DP:RO:AO:SQ:GL 0/1:9:8:1:0.70:64:47:16:8.25:-3,-2,-20 0/0:0:0:0:-0.00:112:112:0:.:-5,-25,-78
X 6146702 9629_2 C C]18:64284796] 8.25 . TOOL=LUMPY;SVTYPE=BND;STR=++:11;IMPRECISE;CIPOS=0,0;CIEND=-1,1;MATEID=9629_1;EVENT=9629;SUP=9;PESUP=8;SRSUP=1;EVTYPE=PE,SR;CSQ=upstream_gene_variant|||ENSG00000146938|NLGN4X|ENST00000381092||||-/816|protein_coding,5_prime_UTR_variant|||ENSG00000146938|NLGN4X|ENST00000381095|1/6|||-/816|protein_coding,upstream_gene_variant|||ENSG00000146938|NLGN4X|ENST00000469740|||||processed_transcript,upstream_gene_variant|||ENSG00000146938|NLGN4X|ENST00000381093||||-/836|protein_coding,upstream_gene_variant|||ENSG00000146938|NLGN4X|ENST00000538097||||-/816|protein_coding,upstream_gene_variant|||ENSG00000146938|NLGN4X|ENST00000275857||||-/816|protein_coding GT:SUP:PE:SR:GQ:DP:RO:AO:SQ:GL 0/1:9:8:1:0.70:64:47:16:8.25:-3,-2,-20 0/0:0:0:0:-0.00:112:112:0:.:-5,-25,-78
|
