1##fileformat=VCFv4.2 2##ALT=<ID=CPX,Description="Complex rearrangement of reference sequence"> 3##ALT=<ID=DEL,Description="Deletion relative to the reference"> 4##ALT=<ID=DUP,Description="Region of elevated copy number relative to the reference"> 5##ALT=<ID=DUP:INV,Description="Region of elevated copy number relative to the reference, with some copies inverted"> 6##ALT=<ID=INS,Description="Insertion of novel sequence relative to the reference"> 7##ALT=<ID=INV,Description="Inversion of reference sequence"> 8##INFO=<ID=ALIGN_LENGTHS,Number=.,Type=Integer,Description="Minimum lengths of the flanking aligned region from each contig alignment"> 9##INFO=<ID=ALT_ARRANGEMENT,Number=.,Type=String,Description="For CPX variants only; specifies how reference segments given in SEGMENTS are re-arranged"> 10##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants"> 11##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants"> 12##INFO=<ID=CONTRACTION,Number=0,Type=Flag,Description="Tandem repeats contraction compared to reference"> 13##INFO=<ID=CPX_EVENT,Number=.,Type=String,Description="ID(s) of CPX event(s) from which current simple variant record is extracted"> 14##INFO=<ID=CTG_GOOD_NONCANONICAL_MAPPING,Number=.,Type=String,Description="Good mapping of evidence contigs as listed in CTG_NAMES to non-canonical reference chromosomes that could potentially offer better explanation of the assembly contig without the SV record. One for each evidence assembly contig, if available; otherwise a \".\". If no evidence contig has such mapping, this annotation is omitted for the record."> 15##INFO=<ID=CTG_NAMES,Number=.,Type=String,Description="Name of local assembly contigs supporting this variant, formatted as \"asm%06d:tig%05d\""> 16##INFO=<ID=DUP_ANNOTATIONS_IMPRECISE,Number=0,Type=Flag,Description="Whether the duplication annotations are from an experimental optimization procedure"> 17##INFO=<ID=DUP_IMPRECISE_AFFECTED_RANGE,Number=.,Type=String,Description="Affected reference range for duplications annotated with the flag DUP_ANNOTATIONS_IMPRECISE"> 18##INFO=<ID=DUP_NUM,Number=R,Type=Integer,Description="Number of times the sequence is duplicated on reference and on the alternate alleles"> 19##INFO=<ID=DUP_ORIENTATIONS,Number=A,Type=String,Description="Orientations of the duplicated sequence on alt allele relative to the copy on ref; one group for each alt allele (currently only available for inverted duplication variants)"> 20##INFO=<ID=DUP_REPEAT_UNIT_REF_SPAN,Number=1,Type=String,Description="Reference span of the suspected repeated unit in a tandem duplication"> 21##INFO=<ID=DUP_SEQ_CIGARS,Number=.,Type=String,Description="CIGARs of the repeated sequence on the locally-assembled contigs when aligned to DUP_REPEAT_UNIT_REF_SPAN (currently only available for repeats when DUP_ANNOTATIONS_IMPRECISE is false)"> 22##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval"> 23##INFO=<ID=EXPANSION,Number=0,Type=Flag,Description="Tandem repeats expansion compared to reference"> 24##INFO=<ID=EXTERNAL_CNV_CALLS,Number=1,Type=String,Description="Comma-delimited list of external copy number calls that overlap with this variant in format ID:CN:CNQ"> 25##INFO=<ID=HOMLEN,Number=1,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints"> 26##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints"> 27##INFO=<ID=HQ_MAPPINGS,Number=1,Type=Integer,Description="Number of high-quality contig alignments that support the variant"> 28##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation"> 29##INFO=<ID=INSLEN,Number=A,Type=Integer,Description="Length of inserted sequence (note for duplication records, this does not count the extra copies of the duplicated sequence)"> 30##INFO=<ID=INSSEQ,Number=.,Type=String,Description="Inserted sequence at the breakpoint"> 31##INFO=<ID=INSSEQ_MAP,Number=.,Type=String,Description="Alignments of inserted sequence"> 32##INFO=<ID=INV33,Number=0,Type=Flag,Description="Whether the event represents a 3' to 5' breakpoint"> 33##INFO=<ID=INV55,Number=0,Type=Flag,Description="Whether the event represents a 5' to 3' breakpoint"> 34##INFO=<ID=LINK,Number=.,Type=String,Description="ID(s) of other variants that are linked to this record, i.e. they constitute a larger more complex variant"> 35##INFO=<ID=MAPPING_QUALITIES,Number=.,Type=Integer,Description="Mapping qualities of the contig alignments that support the variant"> 36##INFO=<ID=MATEID,Number=.,Type=String,Description="ID(s) for mate(s) of a BND record"> 37##INFO=<ID=MAX_ALIGN_LENGTH,Number=1,Type=Integer,Description="Maximum of the values listed in ALIGN_LENGTHS"> 38##INFO=<ID=READ_PAIR_SUPPORT,Number=1,Type=Integer,Description="Number of discordant read pairs supporting the variant"> 39##INFO=<ID=SEGMENTS,Number=.,Type=String,Description="For CPX variants only; segments of reference that are rearranged"> 40##INFO=<ID=SEQ_ALT_HAPLOTYPE,Number=A,Type=Character,Description="Alt haplotype sequence, one per alt allele"> 41##INFO=<ID=SPLIT_READ_SUPPORT,Number=1,Type=Integer,Description="Number of split read supplementary mappings supporting the variant"> 42##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles"> 43##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"> 44##INFO=<ID=TOTAL_MAPPINGS,Number=1,Type=Integer,Description="Number of local assembly contigs supporting the variant, i.e. number of entries in CTG_NAMES"> 45##FILTER=<ID=LOW_MQ,Description="Assembly evidence based record that whose maximum value specified in MAPPING_QUALITIES is lower than user specified threshold"> 46##FILTER=<ID=SHORT_ALN,Description="Assembly evidence based record that whose MAX_ALIGN_LENGTH value is lower than user specified threshold"> 47##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number genotype for imprecise events"> 48##FORMAT=<ID=CNQ,Number=1,Type=Float,Description="Copy number genotype quality for imprecise events"> 49##contig=<ID=chr20,length=64444167,assembly=38> 50##contig=<ID=chr21,length=46709983,assembly=38> 51#CHROM POS ID REF ALT QUAL FILTER INFO 52chr20 12558793 INS_chr20_12558793_12558809_CPX_DERIVED AAAAAAAAAAAAAAAAA <INS> . . CPX_EVENT=CPX_chr20:12558793-12558810;CTG_NAMES=asm027960:tig00003;END=12558809;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=597;SVLEN=133;SVTYPE=INS 53chr20 18675720 INS_chr20_18675720_18675720_CPX_DERIVED A <INS> . . CPX_EVENT=CPX_chr20:18675721-18675877;CTG_NAMES=asm028012:tig00004;END=18675720;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=564;SVLEN=408;SVTYPE=INS 54chr20 20269131 DEL_chr20_20269131_20269198_CPX_DERIVED A <DEL> . . CPX_EVENT=CPX_chr20:20269131-20269199;CTG_NAMES=asm028026:tig00000;END=20269198;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=40;SVLEN=-67;SVTYPE=DEL 55chr20 28561412 INS_chr20_28561412_28561412_CPX_DERIVED A <INS> . . CPX_EVENT=CPX_chr20:28561412-28561576;CTG_NAMES=asm008294:tig00014;END=28561412;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=416;SVLEN=75;SVTYPE=INS 56chr20 28561575 INS_chr20_28561575_28561575_CPX_DERIVED A <INS> . . CPX_EVENT=CPX_chr20:28561412-28561576;CTG_NAMES=asm008294:tig00014;END=28561575;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=416;SVLEN=75;SVTYPE=INS 57chr20 51740560 INS_chr20_51740560_51740560_CPX_DERIVED A <INS> . . CPX_EVENT=CPX_chr20:51740560-51740561;CTG_NAMES=asm028558:tig00002,asm028558:tig00003;END=51740560;MAPPING_QUALITIES=60,60;MAX_ALIGN_LENGTH=1104;SVLEN=549;SVTYPE=INS 58chr20 51740560 INS_chr20_51740560_51740560_CPX_DERIVED A <INS> . . CPX_EVENT=CPX_chr20:51740560-51741035;CTG_NAMES=asm028558:tig00000,asm028558:tig00001;END=51740560;MAPPING_QUALITIES=60,60;MAX_ALIGN_LENGTH=895;SVLEN=549;SVTYPE=INS 59chr20 51741034 INS_chr20_51741034_51741034_CPX_DERIVED T <INS> . . CPX_EVENT=CPX_chr20:51740560-51741035;CTG_NAMES=asm028558:tig00000,asm028558:tig00001;END=51741034;MAPPING_QUALITIES=60,60;MAX_ALIGN_LENGTH=895;SVLEN=50;SVTYPE=INS 60chr20 54849491 INS_chr20_54849491_54849491_CPX_DERIVED C <INS> . . CPX_EVENT=CPX_chr20:54849491-54849615;CTG_NAMES=asm028586:tig00000;END=54849491;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=88;SVLEN=140;SVTYPE=INS 61chr20 54849491 DEL_chr20_54849491_54849614_CPX_DERIVED C <DEL> . . CPX_EVENT=CPX_chr20:54849491-54849615;CTG_NAMES=asm028586:tig00000;END=54849614;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=88;SVLEN=-123;SVTYPE=DEL 62chr20 58695019 INS_chr20_58695019_58695019_CPX_DERIVED G <INS> . . CPX_EVENT=CPX_chr20:58695019-58695020;CTG_NAMES=asm028638:tig00002;END=58695019;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=82;SVLEN=549;SVTYPE=INS 63chr20 64097041 INS_chr20_64097041_64097041_CPX_DERIVED A <INS> . . CPX_EVENT=CPX_chr20:64096905-64097041;CTG_NAMES=asm028821:tig00001;END=64097041;MAPPING_QUALITIES=54;MAX_ALIGN_LENGTH=166;SVLEN=318;SVTYPE=INS 64