Type ID Version Number of files Size in bytes (total) Meta
gene_score gene_properties/gene_scores/Iossifov_Wigler_PNAS_2015 0 6 7.8 MB
None
gene_score gene_properties/gene_scores/LGD 0 7 531.57 KB
None
gene_score gene_properties/gene_scores/RVIS 0 7 449.81 KB
None
gene_score gene_properties/gene_scores/SFARI_gene_score 0 6 124.3 KB
None
gene_score gene_properties/gene_scores/Satterstrom_Buxbaum_Cell_2020 0 6 613.11 KB
None
gene_score gene_properties/gene_scores/pLI 0 7 892.66 KB
None
gene_score gene_properties/gene_scores/pRec 0 7 894.5 KB
None
gene_set gene_properties/gene_sets/GO 0 4 12.07 MB
None
gene_set gene_properties/gene_sets/MSigDB_curated 0 3 3.12 MB
None
gene_set gene_properties/gene_sets/autism 0 7 4.37 KB
None
gene_set gene_properties/gene_sets/disease 0 3 66.76 KB
None
gene_set gene_properties/gene_sets/domain 0 3 391.19 KB
None
gene_set gene_properties/gene_sets/main 0 17 103.89 KB
None
gene_set gene_properties/gene_sets/miRNA 0 4 1.6 MB
None
gene_set gene_properties/gene_sets/miRNA_Darnell 0 3 95.15 KB
None
gene_set gene_properties/gene_sets/relevant 0 15 101.75 KB
None
gene_set gene_properties/gene_sets/sfari 0 11 11.53 KB
None
gene_set gene_properties/gene_sets/spark 0 5 1.22 KB
None
gene_models hg19/gene_models/ccds_v201309 0 4 2.56 MB
None
gene_models hg19/gene_models/knownGene_v201304 0 4 5.49 MB
None
gene_models hg19/gene_models/refGeneMito_v201309 0 4 3.97 MB
None
gene_models hg19/gene_models/refGene_v201309 0 4 3.97 MB
None
gene_models hg19/gene_models/refGene_v20190211 0 4 5.47 MB
None
genome hg19/genomes/GATK_ResourceBundle_5777_b37_phiX174 0 93 2.94 GB

HG19 Reference Genome

Default HG19 reference genome used by GPF
np_score hg19/scores/CADD 0 18 79.37 GB

CADD

Downloaded from https://cadd.gs.washington.edu/download ;

Higher values of raw scores have relative meaning that a variant is more likely to be simulated (or "not observed") and therefore more likely to have deleterious effects.

Scaled scores are PHRED-like (-10*log10(rank/total)) scaled C-score ranking a variant relative to all possible substitutions of the human genome (8.6x10^9).
position_score hg19/scores/FitCons-i6-merged 0 15 105.2 MB

TODO
position_score hg19/scores/FitCons2_E035 0 15 291.53 MB

TODO
position_score hg19/scores/FitCons2_E067 0 15 260.98 MB

TODO
position_score hg19/scores/FitCons2_E068 0 15 270.24 MB

TODO
position_score hg19/scores/FitCons2_E069 0 15 262.14 MB

TODO
position_score hg19/scores/FitCons2_E070 0 15 262.34 MB

TODO
position_score hg19/scores/FitCons2_E071 0 15 255.47 MB

TODO
position_score hg19/scores/FitCons2_E072 0 15 257.62 MB

TODO
position_score hg19/scores/FitCons2_E073 0 15 266.96 MB

TODO
position_score hg19/scores/FitCons2_E074 0 15 262.13 MB

TODO
position_score hg19/scores/FitCons2_E081 0 15 276.05 MB

TODO
position_score hg19/scores/FitCons2_E082 0 15 278.9 MB

TODO
position_score hg19/scores/Linsight 0 15 1.35 GB

TODO
np_score hg19/scores/MPC 0 14 2.26 GB

TODO

tabix -s 1 -b 2 -e 2 -f fordistconstraintofficialmpcvalues_v2.txt.gz
position_score hg19/scores/phastCons46_placentals 0 15 10.55 GB

phastCons46way placentals

This score is from:

http://hgdownload.soe.ucsc.edu/goldenPath/hg19/phastCons46way/README.txt

This directory contains compressed phastCons scores for multiple alignments of 45 vertebrate genomes to the human genome, plus an alternate set of scores for the primates subset of species in the alignments, and an alternate set of scores for the placental mammal subset of species in the alignments.

For a description of the phastCons fixed step wiggle data file format, see: http://genome.ucsc.edu/goldenPath/help/phastCons.html

The multiple alignments and methods description are at: http://hgdownload.soe.ucsc.edu/goldenPath/hg19/multiz46way/

For a description of the phastCons data file format, see: http://genome.ucsc.edu/goldenPath/help/phastCons.html

Assemblies used in these alignments:

  • Human Homo sapiens Feb. 2009 hg19/GRCh37
  • Chimp Pan troglodytes Mar. 2006 panTro2
  • Gorilla Gorilla gorilla gorilla Oct. 2008 gorGor1
  • Orangutan Pongo pygmaeus abelii July 2007 ponAbe2
  • Rhesus Macaca mulatta Jan. 2006 rheMac2
  • Baboon Papio hamadryas Nov. 2008 papHam1
  • Marmoset Callithrix jacchus June 2007 calJac1
  • Tarsier Tarsius syrichta Aug. 2008 tarSyr1
  • Mouse lemur Microcebus murinus Jul. 2007 micMur1
  • Bushbaby Otolemur garnettii Dec. 2006 otoGar1
  • Tree shrew Tupaia belangeri Dec. 2006 tupBel1
  • Mouse Mus musculus July 2007 mm9
  • Rat Rattus norvegicus Nov. 2004 rn4
  • Kangaroo rat Dipodomys ordii Jul. 2008 dipOrd1
  • Guinea Pig Cavia porcellus Feb. 2008 cavPor3
  • Squirrel Spermophilus tridecemlineatus Feb. 2008 speTri1
  • Rabbit Oryctolagus cuniculus Apr. 2009 oryCun2
  • Pika Ochotona princeps Jul. 2008 ochPri2
  • Alpaca Vicugna pacos Jul. 2008 vicPac1
  • Dolphin Tursiops truncatus Feb. 2008 turTru1
  • Cow Bos taurus Oct. 2007 bosTau4
  • Horse Equus caballus Sep. 2007 equCab2
  • Cat Felis catus Mar. 2006 felCat3
  • Dog Canis lupus familiaris May 2005 canFam2
  • Microbat Myotis lucifugus Mar. 2006 myoLuc1
  • Megabat Pteropus vampyrus Jul. 2008 pteVam1
  • Hedgehog Erinaceus europaeus June 2006 eriEur1
  • Shrew Sorex araneus June 2006 sorAra1
  • Elephant Loxodonta africana Jul. 2009 loxAfr3
  • Rock hyrax Procavia capensis Jul. 2008 proCap1
  • Tenrec Echinops telfairi July 2005 echTel1
  • Armadillo Dasypus novemcinctus Jul. 2008 dasNov2
  • Sloth Choloepus hoffmanni Jul. 2008 choHof1
  • Wallaby Macropus eugenii Nov. 2007 macEug1
  • Opossum Monodelphis domestica Oct. 2006 monDom5
  • Platypus Ornithorhynchus anatinus Mar. 2007 ornAna1
  • Chicken Gallus gallus May 2006 galGal3
  • Zebra finch Taeniopygia guttata Jul. 2008 taeGut1
  • Lizard Anolis carolinensis Feb. 2007 anoCar1
  • X. tropicalis Xenopus tropicalis Aug. 2005 xenTro2
  • Tetraodon Tetraodon nigroviridis Mar. 2007 tetNig2
  • Fugu Takifugu rubripes Oct. 2004 fr2
  • Stickleback Gasterosteus aculeatus Feb. 2006 gasAcu1
  • Medaka Oryzias latipes Oct. 2005 oryLat2
  • Zebrafish Danio rerio Dec. 2008 danRer6
  • Lamprey Petromyzon marinus Mar. 2007 petMar1
position_score hg19/scores/phastCons46_primates 0 15 14.02 GB

phastCons46way primates

This score is from:

http://hgdownload.soe.ucsc.edu/goldenPath/hg19/phastCons46way/README.txt

This directory contains compressed phastCons scores for multiple alignments of 45 vertebrate genomes to the human genome, plus an alternate set of scores for the primates subset of species in the alignments, and an alternate set of scores for the placental mammal subset of species in the alignments.

For a description of the phastCons fixed step wiggle data file format, see: http://genome.ucsc.edu/goldenPath/help/phastCons.html

The multiple alignments and methods description are at: http://hgdownload.soe.ucsc.edu/goldenPath/hg19/multiz46way/

For a description of the phastCons data file format, see: http://genome.ucsc.edu/goldenPath/help/phastCons.html

Assemblies used in these alignments:

  • Human Homo sapiens Feb. 2009 hg19/GRCh37
  • Chimp Pan troglodytes Mar. 2006 panTro2
  • Gorilla Gorilla gorilla gorilla Oct. 2008 gorGor1
  • Orangutan Pongo pygmaeus abelii July 2007 ponAbe2
  • Rhesus Macaca mulatta Jan. 2006 rheMac2
  • Baboon Papio hamadryas Nov. 2008 papHam1
  • Marmoset Callithrix jacchus June 2007 calJac1
  • Tarsier Tarsius syrichta Aug. 2008 tarSyr1
  • Mouse lemur Microcebus murinus Jul. 2007 micMur1
  • Bushbaby Otolemur garnettii Dec. 2006 otoGar1
  • Tree shrew Tupaia belangeri Dec. 2006 tupBel1
  • Mouse Mus musculus July 2007 mm9
  • Rat Rattus norvegicus Nov. 2004 rn4
  • Kangaroo rat Dipodomys ordii Jul. 2008 dipOrd1
  • Guinea Pig Cavia porcellus Feb. 2008 cavPor3
  • Squirrel Spermophilus tridecemlineatus Feb. 2008 speTri1
  • Rabbit Oryctolagus cuniculus Apr. 2009 oryCun2
  • Pika Ochotona princeps Jul. 2008 ochPri2
  • Alpaca Vicugna pacos Jul. 2008 vicPac1
  • Dolphin Tursiops truncatus Feb. 2008 turTru1
  • Cow Bos taurus Oct. 2007 bosTau4
  • Horse Equus caballus Sep. 2007 equCab2
  • Cat Felis catus Mar. 2006 felCat3
  • Dog Canis lupus familiaris May 2005 canFam2
  • Microbat Myotis lucifugus Mar. 2006 myoLuc1
  • Megabat Pteropus vampyrus Jul. 2008 pteVam1
  • Hedgehog Erinaceus europaeus June 2006 eriEur1
  • Shrew Sorex araneus June 2006 sorAra1
  • Elephant Loxodonta africana Jul. 2009 loxAfr3
  • Rock hyrax Procavia capensis Jul. 2008 proCap1
  • Tenrec Echinops telfairi July 2005 echTel1
  • Armadillo Dasypus novemcinctus Jul. 2008 dasNov2
  • Sloth Choloepus hoffmanni Jul. 2008 choHof1
  • Wallaby Macropus eugenii Nov. 2007 macEug1
  • Opossum Monodelphis domestica Oct. 2006 monDom5
  • Platypus Ornithorhynchus anatinus Mar. 2007 ornAna1
  • Chicken Gallus gallus May 2006 galGal3
  • Zebra finch Taeniopygia guttata Jul. 2008 taeGut1
  • Lizard Anolis carolinensis Feb. 2007 anoCar1
  • X. tropicalis Xenopus tropicalis Aug. 2005 xenTro2
  • Tetraodon Tetraodon nigroviridis Mar. 2007 tetNig2
  • Fugu Takifugu rubripes Oct. 2004 fr2
  • Stickleback Gasterosteus aculeatus Feb. 2006 gasAcu1
  • Medaka Oryzias latipes Oct. 2005 oryLat2
  • Zebrafish Danio rerio Dec. 2008 danRer6
  • Lamprey Petromyzon marinus Mar. 2007 petMar1
position_score hg19/scores/phastCons46_vertebrates 0 15 10.81 GB

phastCons46way vertebrates

This score is from:

http://hgdownload.soe.ucsc.edu/goldenPath/hg19/phastCons46way/README.txt

This directory contains compressed phastCons scores for multiple alignments of 45 vertebrate genomes to the human genome, plus an alternate set of scores for the primates subset of species in the alignments, and an alternate set of scores for the placental mammal subset of species in the alignments.

For a description of the phastCons fixed step wiggle data file format, see: http://genome.ucsc.edu/goldenPath/help/phastCons.html

The multiple alignments and methods description are at: http://hgdownload.soe.ucsc.edu/goldenPath/hg19/multiz46way/

For a description of the phastCons data file format, see: http://genome.ucsc.edu/goldenPath/help/phastCons.html

Assemblies used in these alignments:

  • Human Homo sapiens Feb. 2009 hg19/GRCh37
  • Chimp Pan troglodytes Mar. 2006 panTro2
  • Gorilla Gorilla gorilla gorilla Oct. 2008 gorGor1
  • Orangutan Pongo pygmaeus abelii July 2007 ponAbe2
  • Rhesus Macaca mulatta Jan. 2006 rheMac2
  • Baboon Papio hamadryas Nov. 2008 papHam1
  • Marmoset Callithrix jacchus June 2007 calJac1
  • Tarsier Tarsius syrichta Aug. 2008 tarSyr1
  • Mouse lemur Microcebus murinus Jul. 2007 micMur1
  • Bushbaby Otolemur garnettii Dec. 2006 otoGar1
  • Tree shrew Tupaia belangeri Dec. 2006 tupBel1
  • Mouse Mus musculus July 2007 mm9
  • Rat Rattus norvegicus Nov. 2004 rn4
  • Kangaroo rat Dipodomys ordii Jul. 2008 dipOrd1
  • Guinea Pig Cavia porcellus Feb. 2008 cavPor3
  • Squirrel Spermophilus tridecemlineatus Feb. 2008 speTri1
  • Rabbit Oryctolagus cuniculus Apr. 2009 oryCun2
  • Pika Ochotona princeps Jul. 2008 ochPri2
  • Alpaca Vicugna pacos Jul. 2008 vicPac1
  • Dolphin Tursiops truncatus Feb. 2008 turTru1
  • Cow Bos taurus Oct. 2007 bosTau4
  • Horse Equus caballus Sep. 2007 equCab2
  • Cat Felis catus Mar. 2006 felCat3
  • Dog Canis lupus familiaris May 2005 canFam2
  • Microbat Myotis lucifugus Mar. 2006 myoLuc1
  • Megabat Pteropus vampyrus Jul. 2008 pteVam1
  • Hedgehog Erinaceus europaeus June 2006 eriEur1
  • Shrew Sorex araneus June 2006 sorAra1
  • Elephant Loxodonta africana Jul. 2009 loxAfr3
  • Rock hyrax Procavia capensis Jul. 2008 proCap1
  • Tenrec Echinops telfairi July 2005 echTel1
  • Armadillo Dasypus novemcinctus Jul. 2008 dasNov2
  • Sloth Choloepus hoffmanni Jul. 2008 choHof1
  • Wallaby Macropus eugenii Nov. 2007 macEug1
  • Opossum Monodelphis domestica Oct. 2006 monDom5
  • Platypus Ornithorhynchus anatinus Mar. 2007 ornAna1
  • Chicken Gallus gallus May 2006 galGal3
  • Zebra finch Taeniopygia guttata Jul. 2008 taeGut1
  • Lizard Anolis carolinensis Feb. 2007 anoCar1
  • X. tropicalis Xenopus tropicalis Aug. 2005 xenTro2
  • Tetraodon Tetraodon nigroviridis Mar. 2007 tetNig2
  • Fugu Takifugu rubripes Oct. 2004 fr2
  • Stickleback Gasterosteus aculeatus Feb. 2006 gasAcu1
  • Medaka Oryzias latipes Oct. 2005 oryLat2
  • Zebrafish Danio rerio Dec. 2008 danRer6
  • Lamprey Petromyzon marinus Mar. 2007 petMar1
position_score hg19/scores/phyloP46_placentals 0 15 14.62 GB

phyloP46way placentals

This file is from:

http://hgdownload.soe.ucsc.edu/goldenPath/hg19/phyloP46way/README.txt

This directory contains conservation scoring by phyloP (phylogenetic p-values) from the PHAST package (http://compgen.bscb.cornell.edu/phast/) for multiple alignments of 45 vertebrate genomes to the human genome, plus alternate sets of scores for the primate species and the placental mammal species in the alignments.

The phastCons data can be found at: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/phastCons46way/

The multiple alignments and methods description are at: http://hgdownload.soe.ucsc.edu/goldenPath/hg19/multiz46way/

For more information about this data, see the track description for the Conservation track: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=cons46way

Assemblies used in these alignments:

  • Human Homo sapiens Feb. 2009 hg19/GRCh37
  • Chimp Pan troglodytes Mar. 2006 panTro2
  • Gorilla Gorilla gorilla gorilla Oct. 2008 gorGor1
  • Orangutan Pongo pygmaeus abelii July 2007 ponAbe2
  • Rhesus Macaca mulatta Jan. 2006 rheMac2
  • Baboon Papio hamadryas Nov. 2008 papHam1
  • Marmoset Callithrix jacchus June 2007 calJac1
  • Tarsier Tarsius syrichta Aug. 2008 tarSyr1
  • Mouse lemur Microcebus murinus Jul. 2007 micMur1
  • Bushbaby Otolemur garnettii Dec. 2006 otoGar1
  • Tree shrew Tupaia belangeri Dec. 2006 tupBel1
  • Mouse Mus musculus July 2007 mm9
  • Rat Rattus norvegicus Nov. 2004 rn4
  • Kangaroo rat Dipodomys ordii Jul. 2008 dipOrd1
  • Guinea Pig Cavia porcellus Feb. 2008 cavPor3
  • Squirrel Spermophilus tridecemlineatus Feb. 2008 speTri1
  • Rabbit Oryctolagus cuniculus Apr. 2009 oryCun2
  • Pika Ochotona princeps Jul. 2008 ochPri2
  • Alpaca Vicugna pacos Jul. 2008 vicPac1
  • Dolphin Tursiops truncatus Feb. 2008 turTru1
  • Cow Bos taurus Oct. 2007 bosTau4
  • Horse Equus caballus Sep. 2007 equCab2
  • Cat Felis catus Mar. 2006 felCat3
  • Dog Canis lupus familiaris May 2005 canFam2
  • Microbat Myotis lucifugus Mar. 2006 myoLuc1
  • Megabat Pteropus vampyrus Jul. 2008 pteVam1
  • Hedgehog Erinaceus europaeus June 2006 eriEur1
  • Shrew Sorex araneus June 2006 sorAra1
  • Elephant Loxodonta africana Jul. 2009 loxAfr3
  • Rock hyrax Procavia capensis Jul. 2008 proCap1
  • Tenrec Echinops telfairi July 2005 echTel1
  • Armadillo Dasypus novemcinctus Jul. 2008 dasNov2
  • Sloth Choloepus hoffmanni Jul. 2008 choHof1
  • Wallaby Macropus eugenii Nov. 2007 macEug1
  • Opossum Monodelphis domestica Oct. 2006 monDom5
  • Platypus Ornithorhynchus anatinus Mar. 2007 ornAna1
  • Chicken Gallus gallus May 2006 galGal3
  • Zebra finch Taeniopygia guttata Jul. 2008 taeGut1
  • Lizard Anolis carolinensis Feb. 2007 anoCar1
  • X. tropicalis Xenopus tropicalis Aug. 2005 xenTro2
  • Tetraodon Tetraodon nigroviridis Mar. 2007 tetNig2
  • Fugu Takifugu rubripes Oct. 2004 fr2
  • Stickleback Gasterosteus aculeatus Feb. 2006 gasAcu1
  • Medaka Oryzias latipes Oct. 2005 oryLat2
  • Zebrafish Danio rerio Dec. 2008 danRer6
  • Lamprey Petromyzon marinus Mar. 2007 petMar1
position_score hg19/scores/phyloP46_primates 0 15 10.81 GB

phyloP46way primates

This file is from:

http://hgdownload.soe.ucsc.edu/goldenPath/hg19/phyloP46way/README.txt

This directory contains conservation scoring by phyloP (phylogenetic p-values) from the PHAST package (http://compgen.bscb.cornell.edu/phast/) for multiple alignments of 45 vertebrate genomes to the human genome, plus alternate sets of scores for the primate species and the placental mammal species in the alignments.

The phastCons data can be found at: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/phastCons46way/

The multiple alignments and methods description are at: http://hgdownload.soe.ucsc.edu/goldenPath/hg19/multiz46way/

For more information about this data, see the track description for the Conservation track: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=cons46way

Assemblies used in these alignments:

  • Human Homo sapiens Feb. 2009 hg19/GRCh37
  • Chimp Pan troglodytes Mar. 2006 panTro2
  • Gorilla Gorilla gorilla gorilla Oct. 2008 gorGor1
  • Orangutan Pongo pygmaeus abelii July 2007 ponAbe2
  • Rhesus Macaca mulatta Jan. 2006 rheMac2
  • Baboon Papio hamadryas Nov. 2008 papHam1
  • Marmoset Callithrix jacchus June 2007 calJac1
  • Tarsier Tarsius syrichta Aug. 2008 tarSyr1
  • Mouse lemur Microcebus murinus Jul. 2007 micMur1
  • Bushbaby Otolemur garnettii Dec. 2006 otoGar1
  • Tree shrew Tupaia belangeri Dec. 2006 tupBel1
  • Mouse Mus musculus July 2007 mm9
  • Rat Rattus norvegicus Nov. 2004 rn4
  • Kangaroo rat Dipodomys ordii Jul. 2008 dipOrd1
  • Guinea Pig Cavia porcellus Feb. 2008 cavPor3
  • Squirrel Spermophilus tridecemlineatus Feb. 2008 speTri1
  • Rabbit Oryctolagus cuniculus Apr. 2009 oryCun2
  • Pika Ochotona princeps Jul. 2008 ochPri2
  • Alpaca Vicugna pacos Jul. 2008 vicPac1
  • Dolphin Tursiops truncatus Feb. 2008 turTru1
  • Cow Bos taurus Oct. 2007 bosTau4
  • Horse Equus caballus Sep. 2007 equCab2
  • Cat Felis catus Mar. 2006 felCat3
  • Dog Canis lupus familiaris May 2005 canFam2
  • Microbat Myotis lucifugus Mar. 2006 myoLuc1
  • Megabat Pteropus vampyrus Jul. 2008 pteVam1
  • Hedgehog Erinaceus europaeus June 2006 eriEur1
  • Shrew Sorex araneus June 2006 sorAra1
  • Elephant Loxodonta africana Jul. 2009 loxAfr3
  • Rock hyrax Procavia capensis Jul. 2008 proCap1
  • Tenrec Echinops telfairi July 2005 echTel1
  • Armadillo Dasypus novemcinctus Jul. 2008 dasNov2
  • Sloth Choloepus hoffmanni Jul. 2008 choHof1
  • Wallaby Macropus eugenii Nov. 2007 macEug1
  • Opossum Monodelphis domestica Oct. 2006 monDom5
  • Platypus Ornithorhynchus anatinus Mar. 2007 ornAna1
  • Chicken Gallus gallus May 2006 galGal3
  • Zebra finch Taeniopygia guttata Jul. 2008 taeGut1
  • Lizard Anolis carolinensis Feb. 2007 anoCar1
  • X. tropicalis Xenopus tropicalis Aug. 2005 xenTro2
  • Tetraodon Tetraodon nigroviridis Mar. 2007 tetNig2
  • Fugu Takifugu rubripes Oct. 2004 fr2
  • Stickleback Gasterosteus aculeatus Feb. 2006 gasAcu1
  • Medaka Oryzias latipes Oct. 2005 oryLat2
  • Zebrafish Danio rerio Dec. 2008 danRer6
  • Lamprey Petromyzon marinus Mar. 2007 petMar1
position_score hg19/scores/phyloP46_vertebrates 0 15 14.72 GB

phyloP46way vertebrates

This file is from:

http://hgdownload.soe.ucsc.edu/goldenPath/hg19/phyloP46way/README.txt

This directory contains conservation scoring by phyloP (phylogenetic p-values) from the PHAST package (http://compgen.bscb.cornell.edu/phast/) for multiple alignments of 45 vertebrate genomes to the human genome, plus alternate sets of scores for the primate species and the placental mammal species in the alignments.

The phastCons data can be found at: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/phastCons46way/

The multiple alignments and methods description are at: http://hgdownload.soe.ucsc.edu/goldenPath/hg19/multiz46way/

For more information about this data, see the track description for the Conservation track: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=cons46way

Assemblies used in these alignments:

  • Human Homo sapiens Feb. 2009 hg19/GRCh37
  • Chimp Pan troglodytes Mar. 2006 panTro2
  • Gorilla Gorilla gorilla gorilla Oct. 2008 gorGor1
  • Orangutan Pongo pygmaeus abelii July 2007 ponAbe2
  • Rhesus Macaca mulatta Jan. 2006 rheMac2
  • Baboon Papio hamadryas Nov. 2008 papHam1
  • Marmoset Callithrix jacchus June 2007 calJac1
  • Tarsier Tarsius syrichta Aug. 2008 tarSyr1
  • Mouse lemur Microcebus murinus Jul. 2007 micMur1
  • Bushbaby Otolemur garnettii Dec. 2006 otoGar1
  • Tree shrew Tupaia belangeri Dec. 2006 tupBel1
  • Mouse Mus musculus July 2007 mm9
  • Rat Rattus norvegicus Nov. 2004 rn4
  • Kangaroo rat Dipodomys ordii Jul. 2008 dipOrd1
  • Guinea Pig Cavia porcellus Feb. 2008 cavPor3
  • Squirrel Spermophilus tridecemlineatus Feb. 2008 speTri1
  • Rabbit Oryctolagus cuniculus Apr. 2009 oryCun2
  • Pika Ochotona princeps Jul. 2008 ochPri2
  • Alpaca Vicugna pacos Jul. 2008 vicPac1
  • Dolphin Tursiops truncatus Feb. 2008 turTru1
  • Cow Bos taurus Oct. 2007 bosTau4
  • Horse Equus caballus Sep. 2007 equCab2
  • Cat Felis catus Mar. 2006 felCat3
  • Dog Canis lupus familiaris May 2005 canFam2
  • Microbat Myotis lucifugus Mar. 2006 myoLuc1
  • Megabat Pteropus vampyrus Jul. 2008 pteVam1
  • Hedgehog Erinaceus europaeus June 2006 eriEur1
  • Shrew Sorex araneus June 2006 sorAra1
  • Elephant Loxodonta africana Jul. 2009 loxAfr3
  • Rock hyrax Procavia capensis Jul. 2008 proCap1
  • Tenrec Echinops telfairi July 2005 echTel1
  • Armadillo Dasypus novemcinctus Jul. 2008 dasNov2
  • Sloth Choloepus hoffmanni Jul. 2008 choHof1
  • Wallaby Macropus eugenii Nov. 2007 macEug1
  • Opossum Monodelphis domestica Oct. 2006 monDom5
  • Platypus Ornithorhynchus anatinus Mar. 2007 ornAna1
  • Chicken Gallus gallus May 2006 galGal3
  • Zebra finch Taeniopygia guttata Jul. 2008 taeGut1
  • Lizard Anolis carolinensis Feb. 2007 anoCar1
  • X. tropicalis Xenopus tropicalis Aug. 2005 xenTro2
  • Tetraodon Tetraodon nigroviridis Mar. 2007 tetNig2
  • Fugu Takifugu rubripes Oct. 2004 fr2
  • Stickleback Gasterosteus aculeatus Feb. 2006 gasAcu1
  • Medaka Oryzias latipes Oct. 2005 oryLat2
  • Zebrafish Danio rerio Dec. 2008 danRer6
  • Lamprey Petromyzon marinus Mar. 2007 petMar1
allele_score hg19/variant_frequencies/gnomAD_v2.1.1/exomes 0 50 959.46 MB

gnomAD exomes v2.1.1

Original gnomAD exomes v2.1.1 is downloaded on October 19, 2020.
allele_score hg19/variant_frequencies/gnomAD_v2.1.1/genomes 0 49 12.27 GB

gnomAD genomes v2.1.1 liftover

Original gnomAD genomes v2.1.1 liftover is downloaded on October 19, 2020 from https://gnomad.broadinstitute.org/.

tabix -s 1 -b 2 -e 2 -f gnomad..r2.1.1.extract.tsv.gz
gene_models hg38/gene_models/refGene_v20170601 0 4 5.41 MB

refSeq gene models for HG38 from 20170601
gene_models hg38/gene_models/refSeq_v20200330 0 4 4.14 MB

refSeq gene models for HG38 from 2020-03

Default gene models used by GPF for HG38.
genome hg38/genomes/GRCh38-hg38 0 3375 3.04 GB

HG38 Reference Genome

Default HG38 reference genome used by GPF
np_score hg38/scores/CADD_v1.4 0 27 79.42 GB

CADD GRCh38-v1.4

TODO
np_score hg38/scores/CADD_v1.6 0 21 80.65 GB

CADD GRCh38-v1.6

TODO
allele_score hg38/scores/clinvar_20221105 0 43 115.18 MB

ClinVar resource downloaded on 2022-11-05. Chromosome names are remapped to have chr prefix.

ClinVar is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. ClinVar thus facilitates access to and communication about the relationships asserted between human variation and observed health status, and the history of that interpretation. ClinVar processes submissions reporting variants found in patient samples, assertions made regarding their clinical significance, information about the submitter, and other supporting data. The alleles described in submissions are mapped to reference sequences, and reported according to the HGVS standard. ClinVar then presents the data for interactive users as well as those wishing to use ClinVar in daily workflows and other local applications. ClinVar works in collaboration with interested organizations to meet the needs of the medical genetics community as efficiently and effectively as possible
position_score hg38/scores/phastCons100way 0 14 10.15 GB

phastConst100way

This file is from:

http://hgdownload.cse.ucsc.edu/goldenPath/hg38/phastCons100way/README.txt

This score contains compressed phastCons scores for multiple alignments of 99 vertebrate genomes to the human genome.

For a description of the phastCons fixed step wiggle data file format, see: http://genome.ucsc.edu/goldenPath/help/phastCons.html

Assemblies used in these alignments:

== Primate subset == Human Homo sapiens Dec 2013 GRCh38/hg38 Reference species Chimp Pan troglodytes Feb 2011 CSAC 2.1.4/panTro4 Syntenic net
Gorilla Gorilla gorilla gorilla May 2011 gorGor3.1/gorGor3 Reciprocal best net Orangutan Pongo pygmaeus abelii July 2007 WUGSC 2.0.2/ponAbe2 Reciprocal best net Gibbon Nomascus leucogenys Oct 2012 GGSC Nleu3.0/nomLeu3 Syntenic net
Rhesus Macaca mulatta Oct 2010 BGI CR1.0/rheMac3 Syntenic net
Crab-eating macaque Macaca fascicularis Jun 2013 Macacafascicularis5.0/macFas5 Syntenic net
Baboon Papio hamadryas Mar 2012 Baylor Panu2.0/papAnu2 Reciprocal best net Green monkey Chlorocebus sabaeus Mar 2014 Chlorocebus_sabeus 1.1/chlSab2 Syntenic net
Marmoset Callithrix jacchus Mar 2009 WUGSC 3.2/calJac3 Syntenic net
Squirrel monkey Saimiri boliviensis Oct 2011 Broad/saiBol1 Syntenic net
Bushbaby Otolemur garnettii Mar 2011 Broad/otoGar3 Syntenic net

== Euarchontoglires subset == Chinese tree shrew Tupaia chinensis Jan 2013 TupChi1.0/tupChi1 Syntenic net
Squirrel Spermophilus tridecemlineatus Nov 2011 Broad/speTri2 Syntenic net
Lesser Egyptian jerboa Jaculus jaculus May 2012 JacJac1.0/jacJac1 Syntenic net
Prairie vole Microtus ochrogaster Oct 2012 MicOch1.0/micOch1 Syntenic net
Chinese hamster Cricetulus griseus Jul 2013 Cgriseusv1.0/criGri1 Syntenic net
Golden hamster Mesocricetus auratus Mar 2013 MesAur1.0/mesAur1 Syntenic net
Mouse Mus musculus Dec 2011 GRCm38/mm10 Syntenic net
Rat Rattus norvegicus Jul 2014 RGSC 6.0/rn6 Syntenic net
Naked mole-rat Heterocephalus glaber Jan 2012 Broad HetGlafemale_1.0/hetGla2 Syntenic net
Guinea pig Cavia porcellus Feb 2008 Broad/cavPor3 Syntenic net
Chinchilla Chinchilla lanigera May 2012 ChiLan1.0/chiLan1 Syntenic net
Brush-tailed rat Octodon degus Apr 2012 OctDeg1.0/octDeg1 Syntenic net
Rabbit Oryctolagus cuniculus Apr 2009 Broad/oryCun2 Syntenic net
Pika Ochotona princeps May 2012 OchPri3.0/ochPri3 Syntenic net

== Laurasiatheria subset == Pig Sus scrofa Aug 2011 SGSC Sscrofa10.2/susScr3 Syntenic net
Alpaca Vicugna pacos Mar 2013 Vicugnapacos-2.0.1/vicPac2 Syntenic net
Bactrian camel Camelus ferus Dec 2011 CB1/camFer1 Syntenic net
Dolphin Tursiops truncatus Oct 2011 Baylor Ttru1.4/turTru2 Reciprocal best net Killer whale Orcinus orca Jan 2013 Oorc1.1/orcOrc1 Syntenic net
Tibetan antelope Pantholops hodgsonii May 2013 PHO1.0/panHod1 Syntenic net
Cow Bos taurus Jun 2014 UMD3.1.1/bosTau8 Syntenic net
Sheep Ovis aries Aug 2012 ISGC Oarv3.1/oviAri3 Syntenic net
Domestic goat Capra hircus May 2012 CHIR1.0/capHir1 Syntenic net
Horse Equus caballus Sep 2007 Broad/equCab2 Syntenic net
White rhinoceros Ceratotherium simum May 2012 CerSimSim1.0/cerSim1 Syntenic net
Cat Felis catus Nov 2014 ICGSC Feliscatus 8.0/felCat8 Syntenic net
Dog Canis lupus familiaris Sep 2011 Broad CanFam3.1/canFam3 Syntenic net
Ferret Mustela putorius furo Apr 2011 MusPutFur1.0/musFur1 Syntenic net
Panda Ailuropoda melanoleuca Dec 2009 BGI-Shenzhen 1.0/ailMel1 Syntenic net
Pacific walrus Odobenus rosmarus divergens Jan 2013 Oros1.0/odoRosDiv1 Syntenic net
Weddell seal Leptonychotes weddellii Mar 2013 LepWed1.0/lepWed1 Reciprocal best net Black flying-fox Pteropus alecto Aug 2012 ASM32557v1/pteAle1 Syntenic net
Megabat Pteropus vampyrus Jul 2008 Broad/pteVam1 Reciprocal best net David's myotis bat Myotis davidii Aug 2012 ASM32734v1/myoDav1 Syntenic net
Microbat Myotis lucifugus Jul 2010 Broad Institute Myoluc2.0/myoLuc2 Syntenic net
Big brown bat Eptesicus fuscus Jul 2012 EptFus1.0/eptFus1 Syntenic net
Hedgehog Erinaceus europaeus May 2012 EriEur2.0/eriEur2 Syntenic net
Shrew Sorex araneus Aug 2008 Broad/sorAra2 Syntenic net
Star-nosed mole Condylura cristata Mar 2012 ConCri1.0/conCri1 Syntenic net

== Afrotheria subset == Elephant Loxodonta africana Jul 2009 Broad/loxAfr3 Syntenic net
Cape elephant shrew Elephantulus edwardii Aug 2012 EleEdw1.0/eleEdw1 Syntenic net
Manatee Trichechus manatus latirostris Oct 2011 Broad v1.0/triMan1 Syntenic net
Cape golden mole Chrysochloris asiatica Aug 2012 ChrAsi1.0/chrAsi1 Syntenic net
Tenrec Echinops telfairi Nov 2012 Broad/echTel2 Syntenic net
Aardvark Orycteropus afer afer May 2012 OryAfe1.0/oryAfe1 Syntenic net

== Mammal subset == Armadillo Dasypus novemcinctus Dec 2011 Baylor/dasNov3 Syntenic net
Opossum Monodelphis domestica Oct 2006 Broad/monDom5 Net
Tasmanian devil Sarcophilus harrisii Feb 2011 WTSI Devilref v7.0/sarHar1 Net
Wallaby Macropus eugenii Sep 2009 TWGS Meug1.1/macEug2 Reciprocal best net Platypus Ornithorhynchus anatinus Mar 2007 WUGSC 5.0.1/ornAna1 Reciprocal best net

== Aves subset == Saker falcon Falco cherrug Feb 2013 Fcherrugv1.0/falChe1 Net
Peregrine falcon Falco peregrinus Feb 2013 Fperegrinusv1.0/falPer1 Net
Collared flycatcher Ficedula albicollis Jun 2013 FicAlb1.5/ficAlb2 Net
White-throated sparrow Zonotrichia albicollis Apr 2013 ASM38545v1/zonAlb1 Net
Medium ground finch Geospiza fortis Apr 2012 GeoFor1.0/geoFor1 Net
Zebra finch Taeniopygia guttata Feb 2013 WashU taeGut324/taeGut2 Net
Tibetan ground jay Pseudopodoces humilis Jan 2013 PseHum1.0/pseHum1 Net
Budgerigar Melopsittacus undulatus Sep 2011 WUSTL v6.3/melUnd1 Net
Parrot Amazona vittata Jan 2013 AV1/amaVit1 Net
Scarlet macaw Ara macao Jun 2013 SMACv1.1/araMac1 Net
Rock pigeon Columba livia Feb 2013 Cliv1.0/colLiv1 Net
Mallard duck Anas platyrhynchos Apr 2013 BGIduck1.0/anaPla1 Net
Chicken Gallus gallus Nov 2011 ICGSC Gallusgallus-4.0/galGal4 Net
Turkey Meleagris gallopavo Dec 2009 TGC Turkey2.01/melGal1 Net

== Sarcopterygii subset == American alligator Alligator mississippiensis Aug 2012 allMis0.2/allMis1 Net
Green seaturtle Chelonia mydas Mar 2013 CheMyd1.0/cheMyd1 Net
Painted turtle Chrysemys picta bellii Mar 2014 v3.0.3/chrPic2 Net
Chinese softshell turtle Pelodiscus sinensis Oct 2011 PelSin1.0/pelSin1 Net
Spiny softshell turtle Apalone spinifera May 2013 ASM38561v1/apaSpi1 Net
Lizard Anolis carolinensis May 2010 Broad AnoCar2.0/anoCar2 Net
X. tropicalis Xenopus tropicalis Sep 2012 JGI 7.0/xenTro7 Net
Coelacanth Latimeria chalumnae Aug 2011 Broad/latCha1 Net

== Fish subset == Tetraodon Tetraodon nigroviridis Mar 2007 Genoscope 8.0/tetNig2 Net
Fugu Takifugu rubripes Oct 2011 FUGU5/fr3 Net
Yellowbelly pufferfish Takifugu flavidus May 2013 version 1 of Takifugu flavidus genome/takFla1 Net
Nile tilapia Oreochromis niloticus Jan 2011 Broad oreNil1.1/oreNil2 Net
Princess of Burundi Neolamprologus brichardi May 2011 NeoBri1.0/neoBri1 Net
Burton's mouthbreeder Haplochromis burtoni Oct 2011 AstBur1.0/hapBur1 Net
Zebra mbuna Maylandia zebra Mar 2012 MetZeb1.1/mayZeb1 Net
Pundamilia nyererei Pundamilia nyererei Oct 2011 PunNye1.0/punNye1 Net
Medaka Oryzias latipes Oct 2005 NIG/UT MEDAKA1/oryLat2 Net
Southern platyfish Xiphophorus maculatus Jan 2012 Xiphophorusmaculatus-4.4.2/xipMac1 Net
Stickleback Gasterosteus aculeatus Feb 2006 Broad/gasAcu1 Net
Atlantic cod Gadus morhua May 2010 Genofisk GadMorMay2010/gadMor1 Net
Zebrafish Danio rerio Sep 2014 Zv10/danRer10 Net
Mexican tetra (cavefish) Astyanax mexicanus Apr 2013 Astyanax_mexicanus-1.0.2/astMex1 Net
Spotted gar Lepisosteus oculatus Dec 2011 LepOcu1/lepOcu1 Net
Lamprey Petromyzon marinus Sep 2010 WUGSC 7.0/petMar2 Net

position_score hg38/scores/phastCons20way 0 14 13.6 GB

phastCons20way

This file is from:

http://hgdownload.cse.ucsc.edu/goldenPath/hg38/phastCons20way/README.txt

This score contains compressed phastCons scores for multiple alignments of 19 genome sequences to the human genome.

For a description of the phastCons fixed step wiggle data file format, see: http://genome.ucsc.edu/goldenPath/help/phastCons.html

The multiple alignments and methods description are at: http://hgdownload.cse.ucsc.edu/goldenPath/hg38/multiz20way/

For more information about this data, see the track description for the Conservation track: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=tarSyr2&g=cons20way

Assemblies used in these alignments: (alignment type)

Human - Homo sapiens Dec. 2013 (GRCh38/hg38) reference

Baboon - Papio anubis Mar. 2012 (Baylor Panu2.0/papAnu2) syntenic Bushbaby - Otolemur garnettii Mar. 2011 (Broad/otoGar3) reciprocal best Bonobo - Pan paniscus May. 2012 (Max-Planck/panPan1) reciprocal best Chimp - Pan troglodytes Feb. 2011 (CSAC 2.1.4/panTro4) syntenic Crab-eating macaque - Macaca fascicularis Jun 2013 (Macacafascicularis5.0/macFas5) syntenic Gibbon - Nomascus leucogenys Oct. 2012 (GGSC Nleu3.0/nomLeu3) syntenic Golden snub-nosed monkey - Rhinopithecus roxellana Oct. 2014 (Rroxv1/rhiRox1) reciprocal best Gorilla - Gorilla gorilla gorilla May 2011 (gorGor3.1/gorGor3) reciprocal best Green monkey - Chlorocebus sabaeus Mar. 2014 (Chlorocebussabeus 1.1/chlSab2) syntenic Marmoset - Callithrix jacchus Mar. 2009 (WUGSC 3.2/calJac3) syntenic Mouse lemur - Microcebus murinus Jul. 2007 (Broad/micMur1) reciprocal best Orangutan - Pongo pygmaeus abelii Jul. 2007 (WUGSC 2.0.2/ponAbe2) syntenic Proboscis monkey - Nasalis larvatus Nov. 2014 (Charlie1.0/nasLar1) reciprocal best Rhesus - Macaca mulatta Oct. 2010 (BGI CR1.0/rheMac3) syntenic Squirrel monkey - Saimiri boliviensis Oct. 2011 (Broad/saiBol1) reciprocal best Tarsier - Tarsius syrichta Sep. 2013 (Tarsius_syrichta-2.0.1/tarSyr2) reciprocal best Tree shrew - Tupaia belangeri Dec. 2006 (Broad/tupBel1) reciprocal best Mouse - Mus musculus Dec. 2011 (GRCm38/mm10) syntenic Dog - Canis lupus familiaris Sep. 2011 (Broad CanFam3.1/canFam3) syntenic
position_score hg38/scores/phastCons30way 0 14 12.97 GB

phastCons30way

This file is from:

http://hgdownload.cse.ucsc.edu/goldenPath/hg38/phastCons30way/README.txt

This score contains compressed phastCons scores for multiple alignments of 29 genome sequences to the human genome.

For a description of the phastCons fixed step wiggle data file format, see: http://genome.ucsc.edu/goldenPath/help/phastCons.html

For more information about this data, see the track description for the Conservation track: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=tarSyr2&g=cons30way

Assemblies used in these alignments: (alignment type)

Human - Homo sapiens Dec. 2013 (GRCh38/hg38) (reference) Angolan colobus - Colobus angolensis palliatus Mar. 2015 (Cang.pa1.0/colAng1) (syntenic) Armadillo - Dasypus novemcinctus Dec. 2011 (Baylor/dasNov3) (syntenic) Baboon - Papio anubis Feb. 2013 (Baylor Panu2.0/papAnu3) (reciprocal best) Black lemur - Eulemur macaco Aug. 2015 (EmacacorefEfBWAoneround/eulMac1) (reciprocal best) Black snub-nosed monkey - Rhinopithecus bieti Aug. 2016 (ASM169854v1/rhiBie1) (reciprocal best) Bonobo - Pan paniscus Aug. 2015 (MPI-EVA panpan1.1/panPan2) (syntenic) Bushbaby - Otolemur garnettii Mar. 2011 (Broad/otoGar3) (syntenic) Chimp - Pan troglodytes May 2016 (Pantro 3.0/panTro5) (syntenic) Coquerel's sifaka - Propithecus coquereli Mar. 2015 (Pcoq1.0/proCoq1) (syntenic) Crab-eating macaque - Macaca fascicularis Jun. 2013 (Macacafascicularis5.0/macFas5) (syntenic) Dog - Canis lupus familiaris Sep. 2011 (Broad CanFam3.1/canFam3) (syntenic) Drill - Mandrillus leucophaeus Mar. 2015 (Mleu.le1.0/manLeu1) (syntenic) Gibbon - Nomascus leucogenys Oct. 2012 (GGSC Nleu3.0/nomLeu3) (syntenic) Golden snub-nosed monkey - Rhinopithecus roxellana Oct. 2014 (Rroxv1/rhiRox1) (reciprocal best) Gorilla - Gorilla gorilla gorilla Mar. 2016 (GSMRT3/gorGor5) (syntenic) Green monkey - Chlorocebus sabaeus Mar. 2014 (Chlorocebussabeus 1.1/chlSab2) (syntenic) Ma's night monkey - Aotus nancymaae Jun. 2017 (Anan2.0/aotNan1) (syntenic) Marmoset - Callithrix jacchus March 2009 (WUGSC 3.2/calJac3) (syntenic) Mouse - Mus musculus Dec. 2011 (GRCm38/mm10) (syntenic) Mouse lemur - Microcebus murinus Feb. 2017 (Mmur3.0/micMur3) (syntenic) Orangutan - Pongo pygmaeus abelii July 2007 (WUGSC 2.0.2/ponAbe2) (reciprocal best) Pig-tailed macaque - Macaca nemestrina Mar. 2015 (Mnem1.0/macNem1) (syntenic) Proboscis monkey - Nasalis larvatus Nov. 2014 (Charlie1.0/nasLar1) (reciprocal best) Rhesus - Macaca mulatta Nov. 2015 (BCM Mmul8.0.1/rheMac8) (syntenic) Sclater's lemur - Eulemur flavifrons Aug. 2015 (Eflavifronsk33QCA/eulFla1) (reciprocal best) Sooty mangabey - Cercocebus atys Mar. 2015 (Caty1.0/cerAty1) (syntenic) Squirrel monkey - Saimiri boliviensis Oct. 2011 (Broad/saiBol1) (syntenic) Tarsier - Tarsius syrichta Sep. 2013 (Tarsiussyrichta-2.0.1/tarSyr2) (reciprocal best) White-faced sapajou - Cebus capucinus imitator Apr. 2016 (Cebus_imitator-1.0/cebCap1) (syntenic)
position_score hg38/scores/phastCons7way 0 15 14.64 GB

phastConst7way

Downloaded from http://hgdownload.cse.ucsc.edu/goldenPath/hg38/phastCons7way/

``` Assemblies used in these alignments: (alignment type)

Human - Homo sapiens Dec. 2013 (GRCh38/hg38) reference Chimp - Pan troglodytes Feb. 2011 (GSAC 2.1.4/panTro4) syntenic Rhesus - Macaca mulatta Oct. 2010 (BGI CR_1.0/rheMac3) syntenic Dog - Canis lupus familiaris Sep. 2011 (Broad/canFam3) syntenic Mouse - Mus musculus Dec. 2011 (GRCm38/mm10) syntenic Rat - Rattus norvegicus Mar. 2012 (RGSC Rnor 5.0/rn5) syntenic Opossum - Monodelphis domestica Oct. 2006 (Broad/monDom5) net ```
position_score hg38/scores/phyloP100way 0 14 16.11 GB

phyloP100way

TODO
position_score hg38/scores/phyloP20way 0 14 14.56 GB

phyloP20way

TODO
position_score hg38/scores/phyloP30way 0 14 14.72 GB

phyloP30way

TODO
position_score hg38/scores/phyloP7way 0 14 12.54 GB

phyloP7way

TODO
allele_score hg38/variant_frequencies/SSC_WG38_CSHL_2380 0 19 783.72 MB

TODO

exported from SFARISSCWGS_CSHL using gpf_validation_data/data_hg38/exports/SFARI_SSC_WGS_CSHL_frequency scripts
allele_score hg38/variant_frequencies/gnomAD_v2.1.1_liftover/exomes 0 53 928.28 MB

gnomAD exomes v2.1.1 liftover

Original gnomAD exomes v2.1.1 liftover is downloaded on October 19, 2020.
allele_score hg38/variant_frequencies/gnomAD_v2.1.1_liftover/genomes 0 56 11.53 GB

gnomAD genomes v2.1.1 liftover

Original gnomAD genomes v2.1.1 liftover is downloaded on October 19, 2020 from https://gnomad.broadinstitute.org/.

tabix -s 1 -b 2 -e 2 -f gnomad..r2.1.1.extract.tsv.gz
allele_score hg38/variant_frequencies/gnomAD_v3/genomes 0 28 17.64 GB

gnomAD genomes v3.0

Original gnomAD genomes v3.0 is downloaded on October 17, 2020 from https://gnomad.broadinstitute.org/.

tabix -s 1 -b 2 -e 2 -f gnomad.genomes.r3.0.extract.tsv.gz
liftover_chain liftover/hg19ToHg38 0 6 450.19 KB

Liftover Chain Hg19 to Hg38
liftover_chain liftover/hg38ToHg19 0 6 2.4 MB
None