#wgs stringent
SV remove chr type	chromosome type=special chromosomes
SV allele frequency NGSD	max_af=1.00
SV filter columns	action=FILTER	entries=PASS
SV PE read depth	PE Read Depth=5
SV quality	quality=100
SV CNV overlap	min_ol=0.5	min_size=10000
SV type	Structural variant type=DEL,DUP,INS,INV,BND	disabled
SV genotype affected	genotypes=hom	same_genotype=false	disabled
SV OMIM genes	disabled
SV gene overlap	complete=true	exonic/splicing=true	intronic/near gene=false	disabled
SV compound-heterozygous	mode=n/a	disabled
SV break point density NGSD	disabled
#wgs relaxed
SV remove chr type	chromosome type=special chromosomes
SV allele frequency NGSD	max_af=1.00
SV CNV overlap	min_ol=0.5	min_size=10000	disabled
SV type	Structural variant type=DEL,DUP,INS,INV,BND	disabled
SV genotype affected	genotypes=hom	same_genotype=false	disabled
SV OMIM genes	disabled
SV gene overlap	complete=true	exonic/splicing=true	intronic/near gene=false	disabled
SV compound-heterozygous	mode=n/a	disabled
SV break point density NGSD	disabled
#---
#lrGS stringent
SV remove chr type	chromosome type=special chromosomes
SV allele frequency NGSD	max_af=1
SV filter columns	entries=PASS	action=FILTER
SV quality	quality=30
SV CNV overlap	min_ol=0.5	min_size=10000
SV break point density NGSD	max_density=20	remove_strict=no	only_system_specific=yes
SV-lr support reads	min_support=5
SV type	Structural variant type=DEL,DUP,INS,INV,BND	disabled
SV genotype affected	genotypes=hom	same_genotype=no	disabled
SV OMIM genes	action=FILTER	disabled
SV gene overlap	complete=yes	exonic/splicing=yes	intronic/near gene=no	disabled
SV compound-heterozygous	mode=n/a	disabled
SV break point density NGSD	max_density=30	remove_strict=no	only_system_specific=no	disabled
SV-lr AF	min_af=0.2	max_af=1
#lrGS relaxed
SV remove chr type	chromosome type=special chromosomes
SV allele frequency NGSD	max_af=1
SV filter columns	entries=PASS	action=FILTER	disabled
SV quality	quality=30	disabled
SV CNV overlap	min_ol=0.5	min_size=10000	disabled
SV break point density NGSD	max_density=20	remove_strict=no	only_system_specific=yes	disabled
SV-lr support reads	min_support=5	disabled
SV type	Structural variant type=DEL,DUP,INS,INV,BND	disabled
SV genotype affected	genotypes=hom	same_genotype=no	disabled
SV OMIM genes	action=FILTER	disabled
SV gene overlap	complete=yes	exonic/splicing=yes	intronic/near gene=no	disabled
SV compound-heterozygous	mode=n/a	disabled
SV break point density NGSD	max_density=30	remove_strict=no	only_system_specific=no	disabled
SV-lr AF	min_af=0.2	max_af=1
#---
#exome stringent
SV remove chr type	chromosome type=special chromosomes
SV count NGSD	max_count=30
SV filter columns	action=FILTER	entries=PASS
SV PE read depth	PE Read Depth=5
SV quality	quality=100
SV type	Structural variant type=DEL,DUP,INS,INV,BND	disabled
SV genotype affected	genotypes=hom	same_genotype=false	disabled
SV OMIM genes	disabled
SV gene overlap	complete=true	exonic/splicing=true	intronic/near gene=false	disabled
SV compound-heterozygous	mode=n/a	disabled
SV break point density NGSD	disabled
#exome relaxed
SV remove chr type	chromosome type=special chromosomes
SV count NGSD	max_count=30
SV type	Structural variant type=DEL,DUP,INS,INV,BND	disabled
SV genotype affected	genotypes=hom	same_genotype=false	disabled
SV OMIM genes	disabled
SV gene overlap	complete=true	exonic/splicing=true	intronic/near gene=false	disabled
SV compound-heterozygous	mode=n/a	disabled
SV break point density NGSD	disabled

#---

#trio WGS stringent
SV remove chr type	chromosome type=special chromosomes
SV allele frequency NGSD	max_af=1.00
SV filter columns	action=FILTER	entries=PASS
SV PE read depth	PE Read Depth=5	only_affected=true
SV quality	quality=100
SV type	Structural variant type=DEL,DUP,INS,INV,BND	disabled
SV OMIM genes	disabled
SV gene overlap	complete=true	exonic/splicing=true	intronic/near gene=false
SV trio	types=de-novo,recessive,LOH,comp-het,x-linked	build=hg38
SV break point density NGSD	disabled

#trio WGS relaxed
SV remove chr type	chromosome type=special chromosomes
SV allele frequency NGSD	max_af=1.00
SV type	Structural variant type=DEL,DUP,INS,INV,BND	disabled
SV OMIM genes	disabled
SV gene overlap	complete=true	exonic/splicing=true	intronic/near gene=false	disabled
SV filter columns	action=FILTER	entries=PASS	disabled
SV trio	types=de-novo,recessive,LOH,comp-het,x-linked	build=hg38
SV break point density NGSD	disabled

#trio WES stringent
SV remove chr type	chromosome type=special chromosomes
SV count NGSD	max_count=20
SV filter columns	action=FILTER	entries=PASS
SV PE read depth	PE Read Depth=5	only_affected=true
SV quality	quality=100
SV type	Structural variant type=DEL,DUP,INS,INV,BND	disabled
SV OMIM genes	disabled
SV gene overlap	complete=true	exonic/splicing=true	intronic/near gene=false
SV trio	types=de-novo,recessive,LOH,comp-het,x-linked	build=hg38
SV break point density NGSD	disabled

#trio WES relaxed
SV remove chr type	chromosome type=special chromosomes
SV count NGSD	max_count=20
SV type	Structural variant type=DEL,DUP,INS,INV,BND	disabled
SV OMIM genes	disabled
SV gene overlap	complete=true	exonic/splicing=true	intronic/near gene=false	disabled
SV filter columns	action=FILTER	entries=PASS	disabled
SV trio	types=de-novo,recessive,LOH,comp-het,x-linked	build=hg38
SV break point density NGSD	disabled

#trio lrGS stringent
SV remove chr type	chromosome type=special chromosomes
SV allele frequency NGSD	max_af=1
SV filter columns	entries=PASS	action=FILTER
SV type	Structural variant type=DEL,DUP,INS,INV,BND	disabled
SV OMIM genes	action=FILTER	disabled
SV gene overlap	complete=yes	exonic/splicing=yes	intronic/near gene=no
SV trio	types=de-novo,recessive,LOH,comp-het,x-linked	gender_child=n/a	build=hg38
SV break point density NGSD	max_density=20	remove_strict=no	only_system_specific=no	disabled

#trio lrGS relaxed
SV remove chr type	chromosome type=special chromosomes
SV allele frequency NGSD	max_af=1
SV type	Structural variant type=DEL,DUP,INS,INV,BND	disabled
SV OMIM genes	action=FILTER	disabled
SV gene overlap	complete=yes	exonic/splicing=yes	intronic/near gene=no	disabled
SV filter columns	entries=PASS	action=FILTER	disabled
SV trio	types=de-novo,recessive,LOH,comp-het,x-linked	gender_child=n/a	build=hg38
SV break point density NGSD	max_density=20	remove_strict=no	only_system_specific=no	disabled

#---

#multi-sample recessive
SV remove chr type	chromosome type=special chromosomes
SV count NGSD	max_count=20
SV type	Structural variant type=DEL,DUP,INS,INV,BND	disabled
SV OMIM genes	disabled
SV gene overlap	complete=true	exonic/splicing=true	intronic/near gene=false	disabled
SV filter columns	action=FILTER	entries=PASS	disabled
SV genotype affected	genotypes=hom
SV genotype control	genotypes=het,wt
SV break point density NGSD	disabled

#multi-sample dominant
SV remove chr type	chromosome type=special chromosomes
SV count NGSD	max_count=20
SV type	Structural variant type=DEL,DUP,INS,INV,BND	disabled
SV OMIM genes	disabled
SV gene overlap	complete=true	exonic/splicing=true	intronic/near gene=false	disabled
SV filter columns	action=FILTER	entries=PASS	disabled
SV genotype affected	genotypes=het,hom
SV genotype control	genotypes=wt
SV break point density NGSD	disabled

#---
#somatic
SV SomaticScore	Somaticscore=50	disabled