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igvteam / igv.js

Embeddable genomic visualization component based on the Integrative Genomics Viewer
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BigBed track flattened up on one line #1077

Closed northwestwitch closed 3 years ago

northwestwitch commented 4 years ago

Hello and thanks for the amazing software, we are using it in our repo and our alignments look great!

Some days ago I decided to try to load the bigbed tracks that UCSC is providing as clinvar tracks (http://hgdownload.soe.ucsc.edu/gbdb/hg19/bbi/clinvar/) and I got weird results, see this issue for reference: https://github.com/Clinical-Genomics/scout/issues/1793

Looks like all the variants are displayed on a single line.

This is the track description in UCSC: http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=800793167_hrmbHk3PnFAEufLOaCuuAKssHaP4&c=chr21&g=clinvar

Is it a matter of wrong settings I'm using or the files are not completely supported?

My settings look like this:

type : annotation
format : bigBed
url :  http://hgdownload.soe.ucsc.edu/gbdb/hg19/bbi/clinvar/clinvarMain.bb 
sourceType : file

Thanks for your help!

jrobinso commented 4 years ago

Try setting the display mode to EXPANDED

displayMode: 'EXPANDED'

By default it is set to collapsed. This will put the variants on multiple lines, however its not going to look like the UCSC track you reference. It looks like the display mode there is set to "FULL", which puts every variant on a new line.

northwestwitch commented 4 years ago

Thanks for your answer @jrobinso! I've tried to set the displayMode to EXPANDED or even FULL but the result is exactly the same, all variants on the same line..

jrobinso commented 4 years ago

If they don't overlap they will be on the same line. igv.js does not support "FULL". Can you post a screenshot?

On Fri, Mar 13, 2020 at 12:47 AM Chiara Rasi notifications@github.com wrote:

Thanks for your answer @jrobinso https://github.com/jrobinso! I've tried to set the displayMode to EXPANDED or even FULL but the result is exactly the same, all variants on the same line..

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/igvteam/igv.js/issues/1077#issuecomment-598593597, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAHD2HBWLYX2CMONDY2SY2DRHHQIJANCNFSM4LGPELLA .

northwestwitch commented 4 years ago

Here is how the "EXPANDED" displayMode looks like in the interval: chr21:47408993-47409093

image

But when I read the bigBed in the same interval there are the following variants:

('chr21', 47408977, 47409071, 'g.', '1', '.', '47408977', '47409071', '210,0,0', '1', '94', '0', '584291|NC_000021.8:g.(?_47408978)_(47409071_?)del', 'Pathogenic', '&#9733;&#9734;&#9734;&#9734;&nbsp;&nbsp;<small>based on: criteria provided,single submitter</small>', 'deletion', '1291|COL6A1', '', '', 'RCV000708450', 'N', 'Bethlem myopathy 1', "<a target=_blank href='https://www.ncbi.nlm.nih.gov/medgen/CN029274'>MedGen:CN029274</a>, <a target=_blank href='http://www.omim.org/entry/158810'>OMIM:158810</a>", 'germline', 'GRCh37', '21q22.3', '', '', '1', 'May 14,2018', '', '', 'g.(?_47408978)_(47409071_?)del, Pathogenic, 1 stars, Phenotypes: Bethlem myopathy 1, Origin: germline, 1 submitters', 'PG', '94')
('chr21', 47408995, 47408996, 'A>G', '1', '.', '47408995', '47408996', '210,0,0', '1', '1', '0', '93888|NM_001848.2(COL6A1):c.805-2A>G', 'Pathogenic', '&#9733;&#9734;&#9734;&#9734;&nbsp;&nbsp;<small>based on: criteria provided,single submitter</small>', 'single nucleotide variant', '1291|COL6A1', '398123639', '', 'RCV000180576', 'N', 'not provided', "<a target=_blank href='https://www.ncbi.nlm.nih.gov/medgen/CN517202'>MedGen:CN517202</a>", 'germline', 'GRCh37', '21q22.3', 'NM_001848.2:c.805-2A>G', '', '1', 'Aug 28,2012', '', '', 'c.805-2A>G, Pathogenic, 1 stars, Phenotypes: not provided, Origin: germline, 1 submitters', 'PG', '1')
('chr21', 47408997, 47408998, 'G>A', '1', '.', '47408997', '47408998', '210,0,0', '1', '1', '0', '284383|NM_001848.2(COL6A1):c.805G>A (p.Gly269Arg)', 'Likely pathogenic', '&#9733;&#9734;&#9734;&#9734;&nbsp;&nbsp;<small>based on: criteria provided,single submitter</small>', 'single nucleotide variant', '1291|COL6A1', '886042856', '', 'RCV000404469', 'N', 'not provided', "<a target=_blank href='https://www.ncbi.nlm.nih.gov/medgen/CN517202'>MedGen:CN517202</a>", 'germline', 'GRCh37', '21q22.3', 'NM_001848.2:c.805G>A', 'NP_001839.2:p.Gly269Arg', '1', 'Oct 28,2015', '', '', 'c.805G>A, Likely pathogenic, 1 stars, Phenotypes: not provided, Origin: germline, 1 submitters', 'LP', '1')
('chr21', 47409001, 47409004, 'del', '1', '.', '47409001', '47409004', '210,0,0', '1', '3', '0', '584434|NM_001848.2(COL6A1):c.809_811del (p.Glu270_Arg271delinsGly)', 'Likely pathogenic', '&#9733;&#9734;&#9734;&#9734;&nbsp;&nbsp;<small>based on: criteria provided,single submitter</small>', 'deletion', '1291|COL6A1', '1569518070', '', 'RCV000708567', 'N', 'Bethlem myopathy 1', "<a target=_blank href='https://www.ncbi.nlm.nih.gov/medgen/CN029274'>MedGen:CN029274</a>, <a target=_blank href='http://www.omim.org/entry/158810'>OMIM:158810</a>", 'de novo', 'GRCh37', '21q22.3', 'NM_001848.2:c.809_811del', 'NP_001839.2:p.Glu270_Arg271delinsGly', '1', 'Feb 09,2018', '', '', 'c.809_811del, Likely pathogenic, 1 stars, Phenotypes: Bethlem myopathy 1, Origin: de novo, 1 submitters', 'LP', '3')
('chr21', 47409003, 47409004, 'C>T', '1', '.', '47409003', '47409004', '210,0,0', '1', '1', '0', '497373|NM_001848.2(COL6A1):c.811C>T (p.Arg271Ter)', 'Pathogenic', '&#9733;&#9734;&#9734;&#9734;&nbsp;&nbsp;<small>based on: criteria provided,single submitter</small>', 'single nucleotide variant', '1291|COL6A1', '1391624796', '', 'RCV000591172', 'N', 'not provided', "<a target=_blank href='https://www.ncbi.nlm.nih.gov/medgen/CN517202'>MedGen:CN517202</a>", 'germline', 'GRCh37', '21q22.3', 'NM_001848.2:c.811C>T', 'NP_001839.2:p.Arg271Ter', '1', 'Oct 17,2016', '', '', 'c.811C>T, Pathogenic, 1 stars, Phenotypes: not provided, Origin: germline, 1 submitters', 'PG', '1')
('chr21', 47409005, 47409006, 'A>G', '1', '.', '47409005', '47409006', '0,210,0', '1', '1', '0', '543029|NM_001848.2(COL6A1):c.813A>G (p.Arg271=)', 'Likely benign', '&#9733;&#9734;&#9734;&#9734;&nbsp;&nbsp;<small>based on: criteria provided,single submitter</small>', 'single nucleotide variant', '1291|COL6A1', '748184568', '', 'RCV000653670', 'N', 'not provided', "<a target=_blank href='https://www.ncbi.nlm.nih.gov/medgen/CN517202'>MedGen:CN517202</a>", 'germline', 'GRCh37', '21q22.3', 'NM_001848.2:c.813A>G', 'NP_001839.2:p.Arg271=', '1', 'Apr 26,2018', '', '', 'c.813A>G, Likely benign, 1 stars, Phenotypes: not provided, Origin: germline, 1 submitters', 'LB', '1')
('chr21', 47409006, 47409007, 'G>C', '1', '.', '47409006', '47409007', '210,0,0', '1', '1', '0', '581961|NM_001848.2(COL6A1):c.814G>C (p.Gly272Arg)', 'Pathogenic', '&#9733;&#9734;&#9734;&#9734;&nbsp;&nbsp;<small>based on: criteria provided,single submitter</small>', 'single nucleotide variant', '1291|COL6A1', '398123640', '', 'RCV000705919', 'N', 'Bethlem myopathy 1', "<a target=_blank href='https://www.ncbi.nlm.nih.gov/medgen/CN029274'>MedGen:CN029274</a>, <a target=_blank href='http://www.omim.org/entry/158810'>OMIM:158810</a>", 'germline', 'GRCh37', '21q22.3', 'NM_001848.2:c.814G>C', 'NP_001839.2:p.Gly272Arg', '1', 'Jul 13,2018', '', '', 'c.814G>C, Pathogenic, 1 stars, Phenotypes: Bethlem myopathy 1, Origin: germline, 1 submitters', 'PG', '1')
('chr21', 47409006, 47409007, 'G>A', '1', '.', '47409006', '47409007', '210,0,0', '1', '1', '0', '93889|NM_001848.2(COL6A1):c.814G>A (p.Gly272Ser)', 'Conflicting interpretations of pathogenicity', '&#9733;&#9734;&#9734;&#9734;&nbsp;&nbsp;<small>based on: criteria provided,conflicting interpretations</small>', 'single nucleotide variant', '1291|COL6A1', '398123640', '', 'RCV000415255,RCV000415255,RCV000415255,RCV000079827', 'N', 'EMG abnormality,Limb-girdle muscle weakness,Motor delay,not provided', "Human Phenotype Ontology:HP:0003457, <a target=_blank href='https://www.ncbi.nlm.nih.gov/medgen/C0476403'>MedGen:C0476403</a>, Human Phenotype Ontology:HP:0003325, <a target=_blank href='https://www.ncbi.nlm.nih.gov/medgen/C1858127'>MedGen:C1858127</a>, Human Phenotype Ontology:HP:0001270, <a target=_blank href='https://www.ncbi.nlm.nih.gov/medgen/C1854301'>MedGen:C1854301</a>, <a target=_blank href='https://www.ncbi.nlm.nih.gov/medgen/CN517202'>MedGen:CN517202</a>", 'germline,unknown', 'GRCh37', '21q22.3', 'NM_001848.2:c.814G>A', 'NP_001839.2:p.Gly272Ser', '2', 'Apr 01,2014', '', '', 'c.814G>A, Conflicting interpretations of pathogenicity, 1 stars, Phenotypes: EMG abnormality,Limb-girdle muscle weakness,Motor delay,not provided, Origin: germline,unknown, 2 submitters', 'CF', '1')
('chr21', 47409007, 47409008, 'G>A', '1', '.', '47409007', '47409008', '210,0,0', '1', '1', '0', '419392|NM_001848.2(COL6A1):c.815G>A (p.Gly272Asp)', 'Pathogenic', '&#9733;&#9734;&#9734;&#9734;&nbsp;&nbsp;<small>based on: criteria provided,single submitter</small>', 'single nucleotide variant', '1291|COL6A1', '1064793840', '', 'RCV000481274', 'N', 'not provided', "<a target=_blank href='https://www.ncbi.nlm.nih.gov/medgen/CN517202'>MedGen:CN517202</a>", 'germline', 'GRCh37', '21q22.3', 'NM_001848.2:c.815G>A', 'NP_001839.2:p.Gly272Asp', '1', 'Jul 13,2015', '', '', 'c.815G>A, Pathogenic, 1 stars, Phenotypes: not provided, Origin: germline, 1 submitters', 'PG', '1')
('chr21', 47409013, 47409014, 'C>T', '2', '.', '47409013', '47409014', '128,128,128', '1', '1', '0', '202178|NM_001848.2(COL6A1):c.821C>T (p.Pro274Leu)', 'Uncertain significance', '&#9733;&#9733;&#9734;&#9734;&nbsp;&nbsp;<small>based on: criteria provided,multiple submitters,no conflicts</small>', 'single nucleotide variant', '1291|COL6A1', '201093313', '', 'RCV000184024,RCV000731127', 'N', 'Bethlem myopathy 1,not provided', "<a target=_blank href='https://www.ncbi.nlm.nih.gov/medgen/CN029274'>MedGen:CN029274</a>, <a target=_blank href='http://www.omim.org/entry/158810'>OMIM:158810</a>, <a target=_blank href='https://www.ncbi.nlm.nih.gov/medgen/CN517202'>MedGen:CN517202</a>", 'germline,unknown', 'GRCh37', '21q22.3', 'NM_001848.2:c.821C>T', 'NP_001839.2:p.Pro274Leu', '3', 'Dec 12,2018', '', 'UniProtKB (protein):P12109#VAR_058215', 'c.821C>T, Uncertain significance, 2 stars, Phenotypes: Bethlem myopathy 1,not provided, Origin: germline,unknown, 3 submitters', 'UC', '1')
('chr21', 47409014, 47409015, 'G>A', '1', '.', '47409014', '47409015', '128,128,128', '1', '1', '0', '290607|NM_001848.2(COL6A1):c.822G>A (p.Pro274=)', 'Uncertain significance', '&#9733;&#9734;&#9734;&#9734;&nbsp;&nbsp;<small>based on: criteria provided,single submitter</small>', 'single nucleotide variant', '1291|COL6A1', '886044503', '', 'RCV000350919', 'N', 'not provided', "<a target=_blank href='https://www.ncbi.nlm.nih.gov/medgen/CN517202'>MedGen:CN517202</a>", 'germline', 'GRCh37', '21q22.3', 'NM_001848.2:c.822G>A', 'NP_001839.2:p.Pro274=', '1', 'Sep 13,2016', '', '', 'c.822G>A, Uncertain significance, 1 stars, Phenotypes: not provided, Origin: germline, 1 submitters', 'UC', '1')
('chr21', 47409015, 47409016, 'G>C', '1', '.', '47409015', '47409016', '210,0,0', '1', '1', '0', '598051|NM_001848.2(COL6A1):c.823G>C (p.Gly275Arg)', 'Likely pathogenic', '&#9733;&#9734;&#9734;&#9734;&nbsp;&nbsp;<small>based on: criteria provided,single submitter</small>', 'single nucleotide variant', '1291|COL6A1', '1556425467', '', 'RCV000734346', 'N', 'not provided', "<a target=_blank href='https://www.ncbi.nlm.nih.gov/medgen/CN517202'>MedGen:CN517202</a>", 'germline', 'GRCh37', '21q22.3', 'NM_001848.2:c.823G>C', 'NP_001839.2:p.Gly275Arg', '1', 'Aug 02,2018', '', '', 'c.823G>C, Likely pathogenic, 1 stars, Phenotypes: not provided, Origin: germline, 1 submitters', 'LP', '1')
('chr21', 47409015, 47409016, 'G>T', '1', '.', '47409015', '47409016', '210,0,0', '1', '1', '0', '476439|NM_001848.2(COL6A1):c.823G>T (p.Gly275Trp)', 'Pathogenic', '&#9733;&#9734;&#9734;&#9734;&nbsp;&nbsp;<small>based on: criteria provided,single submitter</small>', 'single nucleotide variant', '1291|COL6A1', '1556425467', '', 'RCV000544305', 'N', 'Bethlem myopathy 1', "<a target=_blank href='https://www.ncbi.nlm.nih.gov/medgen/CN029274'>MedGen:CN029274</a>, <a target=_blank href='http://www.omim.org/entry/158810'>OMIM:158810</a>", 'germline', 'GRCh37', '21q22.3', 'NM_001848.2:c.823G>T', 'NP_001839.2:p.Gly275Trp', '1', 'Sep 12,2016', '', '', 'c.823G>T, Pathogenic, 1 stars, Phenotypes: Bethlem myopathy 1, Origin: germline, 1 submitters', 'PG', '1')
('chr21', 47409016, 47409017, 'G>T', '2', '.', '47409016', '47409017', '210,0,0', '1', '1', '0', '520716|NM_001848.2(COL6A1):c.824G>T (p.Gly275Val)', 'Likely pathogenic', '&#9733;&#9733;&#9734;&#9734;&nbsp;&nbsp;<small>based on: criteria provided,multiple submitters,no conflicts</small>', 'single nucleotide variant', '1291|COL6A1', '1556425468', '', 'RCV000689918,RCV000624350', 'N', 'Bethlem myopathy 1,Inborn genetic diseases', "<a target=_blank href='https://www.ncbi.nlm.nih.gov/medgen/CN029274'>MedGen:CN029274</a>, <a target=_blank href='http://www.omim.org/entry/158810'>OMIM:158810</a>, MeSH:D030342, <a target=_blank href='https://www.ncbi.nlm.nih.gov/medgen/C0950123'>MedGen:C0950123</a>", 'germline', 'GRCh37', '21q22.3', 'NM_001848.2:c.824G>T', 'NP_001839.2:p.Gly275Val', '2', 'Oct 08,2018', '', '', 'c.824G>T, Likely pathogenic, 2 stars, Phenotypes: Bethlem myopathy 1,Inborn genetic diseases, Origin: germline, 2 submitters', 'LP', '1')
('chr21', 47409021, 47409022, 'C>T', '1', '.', '47409021', '47409022', '128,128,128', '1', '1', '0', '598050|NM_001848.2(COL6A1):c.829C>T (p.Pro277Ser)', 'Uncertain significance', '&#9733;&#9734;&#9734;&#9734;&nbsp;&nbsp;<small>based on: criteria provided,single submitter</small>', 'single nucleotide variant', '1291|COL6A1', '747542234', '', 'RCV000734345', 'N', 'not provided', "<a target=_blank href='https://www.ncbi.nlm.nih.gov/medgen/CN517202'>MedGen:CN517202</a>", 'germline', 'GRCh37', '21q22.3', 'NM_001848.2:c.829C>T', 'NP_001839.2:p.Pro277Ser', '1', 'Jul 19,2018', '', '', 'c.829C>T, Uncertain significance, 1 stars, Phenotypes: not provided, Origin: germline, 1 submitters', 'UC', '1')
('chr21', 47409025, 47409026, 'G>A', '1', '.', '47409025', '47409026', '210,0,0', '1', '1', '0', '285457|NM_001848.2(COL6A1):c.833G>A (p.Gly278Glu)', 'Likely pathogenic', '&#9733;&#9734;&#9734;&#9734;&nbsp;&nbsp;<small>based on: criteria provided,single submitter</small>', 'single nucleotide variant', '1291|COL6A1', '886043106', '', 'RCV000401877', 'N', 'not provided', "<a target=_blank href='https://www.ncbi.nlm.nih.gov/medgen/CN517202'>MedGen:CN517202</a>", 'germline', 'GRCh37', '21q22.3', 'NM_001848.2:c.833G>A', 'NP_001839.2:p.Gly278Glu', '1', 'Aug 22,2017', '', '', 'c.833G>A, Likely pathogenic, 1 stars, Phenotypes: not provided, Origin: germline, 1 submitters', 'LP', '1')
('chr21', 47409033, 47409034, 'G>A', '1', '.', '47409033', '47409034', '210,0,0', '1', '1', '0', '17182|NM_001848.2(COL6A1):c.841G>A (p.Gly281Arg)', 'Pathogenic', '&#9733;&#9734;&#9734;&#9734;&nbsp;&nbsp;<small>based on: criteria provided,single submitter</small>', 'single nucleotide variant', '1291|COL6A1', '267606746', '', 'RCV000018722,RCV000497629', 'N', 'Ullrich congenital muscular dystrophy 1,not provided', "<a target=_blank href='https://www.ncbi.nlm.nih.gov/medgen/CN033863'>MedGen:CN033863</a>, <a target=_blank href='http://www.omim.org/entry/254090'>OMIM:254090</a>, <a target=_blank href='https://www.ncbi.nlm.nih.gov/medgen/CN517202'>MedGen:CN517202</a>", 'germline', 'GRCh37', '21q22.3', 'NM_001848.2:c.841G>A', 'NP_001839.2:p.Gly281Arg', '2', 'May 17,2017', '', "<a target=_blank href='http://www.omim.org/entry/120220#0014'>OMIM Allelic Variant:120220.0014</a>, UniProtKB (protein):P12109#VAR_058217", 'c.841G>A, Pathogenic, 1 stars, Phenotypes: Ullrich congenital muscular dystrophy 1,not provided, Origin: germline, 2 submitters', 'PG', '1')
('chr21', 47409034, 47409035, 'G>A', '1', '.', '47409034', '47409035', '210,0,0', '1', '1', '0', '280099|NM_001848.2(COL6A1):c.842G>A (p.Gly281Glu)', 'Pathogenic', '&#9733;&#9734;&#9734;&#9734;&nbsp;&nbsp;<small>based on: criteria provided,single submitter</small>', 'single nucleotide variant', '1291|COL6A1', '886041383', '', 'RCV000387642', 'N', 'not provided', "<a target=_blank href='https://www.ncbi.nlm.nih.gov/medgen/CN517202'>MedGen:CN517202</a>", 'germline', 'GRCh37', '21q22.3', 'NM_001848.2:c.842G>A', 'NP_001839.2:p.Gly281Glu', '1', 'Jul 27,2016', '', '', 'c.842G>A, Pathogenic, 1 stars, Phenotypes: not provided, Origin: germline, 1 submitters', 'PG', '1')
('chr21', 47409038, 47409047, 'del', '1', '.', '47409038', '47409047', '210,0,0', '1', '9', '0', '476440|NM_001848.2(COL6A1):c.846_854del (p.Glu282_Gly284del)', 'Conflicting interpretations of pathogenicity', '&#9733;&#9734;&#9734;&#9734;&nbsp;&nbsp;<small>based on: criteria provided,conflicting interpretations</small>', 'deletion', '1291|COL6A1', '1556425474', '', 'RCV000552183,RCV000596227', 'N', 'Bethlem myopathy 1,not provided', "<a target=_blank href='https://www.ncbi.nlm.nih.gov/medgen/CN029274'>MedGen:CN029274</a>, <a target=_blank href='http://www.omim.org/entry/158810'>OMIM:158810</a>, <a target=_blank href='https://www.ncbi.nlm.nih.gov/medgen/CN517202'>MedGen:CN517202</a>", 'germline', 'GRCh37', '21q22.3', 'NM_001848.2:c.846_854del', 'NP_001839.2:p.Glu282_Gly284del', '2', 'Apr 06,2017', '', '', 'c.846_854del, Conflicting interpretations of pathogenicity, 1 stars, Phenotypes: Bethlem myopathy 1,not provided, Origin: germline, 2 submitters', 'CF', '9')
('chr21', 47409042, 47409043, 'G>A', '2', '.', '47409042', '47409043', '210,0,0', '1', '1', '0', '17180|NM_001848.2(COL6A1):c.850G>A (p.Gly284Arg)', 'Pathogenic', '&#9733;&#9733;&#9734;&#9734;&nbsp;&nbsp;<small>based on: criteria provided,multiple submitters,no conflicts</small>', 'single nucleotide variant', '1291|COL6A1', '121912938', '', 'RCV000180573,RCV000180574,RCV000018720,RCV000079828', 'N', 'Bethlem myopathy 1,Ullrich congenital muscular dystrophy 1,Ullrich congenital muscular dystrophy 1,autosomal dominant,not provided', "<a target=_blank href='https://www.ncbi.nlm.nih.gov/medgen/CN029274'>MedGen:CN029274</a>, <a target=_blank href='http://www.omim.org/entry/158810'>OMIM:158810</a>, <a target=_blank href='https://www.ncbi.nlm.nih.gov/medgen/CN033863'>MedGen:CN033863</a>, <a target=_blank href='http://www.omim.org/entry/254090'>OMIM:254090</a>, <a target=_blank href='https://www.ncbi.nlm.nih.gov/medgen/C4015958'>MedGen:C4015958</a>, <a target=_blank href='https://www.ncbi.nlm.nih.gov/medgen/CN517202'>MedGen:CN517202</a>", 'germline', 'GRCh37', '21q22.3', 'NM_001848.2:c.850G>A', 'NP_001839.2:p.Gly284Arg', '7', 'Dec 10,2018', '', "HGMD:CM050214, <a target=_blank href='http://www.omim.org/entry/120220#0012'>OMIM Allelic Variant:120220.0012</a>, UniProtKB (protein):P12109#VAR_058218", 'c.850G>A, Pathogenic, 2 stars, Phenotypes: Bethlem myopathy 1,Ullrich congenital muscular dystrophy 1,Ullrich congenital muscular dystrophy 1,autosomal dominant,not provided, Origin: germline, 7 submitters', 'PG', '1')
('chr21', 47409049, 47409050, 'del', '0', '.', '47409049', '47409050', '210,0,0', '1', '1', '0', '17177|NM_001848.2(COL6A1):c.857del (p.Pro286fs)', 'Pathogenic', '&#9734;&#9734;&#9734;&#9734;&nbsp;&nbsp;<small>based on: no assertion criteria provided</small>', 'deletion', '1291|COL6A1', '797044457', '', 'RCV000018717', 'N', 'Ullrich congenital muscular dystrophy 1', "<a target=_blank href='https://www.ncbi.nlm.nih.gov/medgen/CN033863'>MedGen:CN033863</a>, <a target=_blank href='http://www.omim.org/entry/254090'>OMIM:254090</a>", 'germline', 'GRCh37', '21q22.3', 'NM_001848.2:c.857del', 'NP_001839.2:p.Pro286fs', '1', 'Sep 01,2005', '', "<a target=_blank href='http://www.omim.org/entry/120220#0009'>OMIM Allelic Variant:120220.0009</a>", 'c.857del, Pathogenic, 0 stars, Phenotypes: Ullrich congenital muscular dystrophy 1, Origin: germline, 1 submitters', 'PG', '1')
jrobinso commented 4 years ago

OK that does look like a problem. Could you post your track configuration below and I will look into this later today. Also, what version of igv.js are you using?

northwestwitch commented 4 years ago

It's very likely that I'm using some wrong parameters in the track settings!

My complete track configuration looks like this:

{                       
                          name: "ClinVar",
                          type: "annotation",
                          format: "bigBed",
                          sourceType: "file",
                          url: "{{ clinvar_snvs.url|replace('%2F','/') }}",
                          displayMode: "EXPANDED",
                          order: Number.MIN_VALUE,
}

where clinvar_snvs is https://hgdownload.soe.ucsc.edu/gbdb/hg38/bbi/clinvar/clinvarMain.bb

First I was using version 2.3, then I switched to 2.4, but the visualization didn't improve.

Thank you so much for the help!

northwestwitch commented 4 years ago

Hi @jrobinso, I was wondering if you had time to take a look at this. I totally understand if you are busy so no rush! :)

jrobinso commented 4 years ago

Sorry, other things intervened. Thanks for the reminder, I will look at it tomorrow.

On Wed, Mar 25, 2020 at 12:22 AM Chiara Rasi notifications@github.com wrote:

Hi @jrobinso https://github.com/jrobinso, I was wondering if you had time to take a look at this. I totally understand if you are busy so no rush! :)

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/igvteam/igv.js/issues/1077#issuecomment-603682091, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAHD2HHTV2QLUSW7JBFVELTRJGWMRANCNFSM4LGPELLA .

northwestwitch commented 4 years ago

Sorry, other things intervened. Thanks for the reminder, I will look at it tomorrow.

Thanks!

jrobinso commented 4 years ago

OK I found the problem, thanks for your patience. Bigbed files were not properly "packed" for expanded mode. Your example figure was in a region with a single long variant, which covered up the smaller variants. See the screenshot below for what it should look like.

The fix will require some testing before release, I will update here when it is released.

Screen Shot 2020-03-25 at 10 01 07 AM
northwestwitch commented 4 years ago

Thank you so much!! 🥇

northwestwitch commented 4 years ago

Hi @jrobinso, we are planning to switch to the new release as soon as it's out, and in the meanwhile we've been using the nightly snapshot (http://igv.org/web/snapshot/dist/igv.js) which contains this bugfix.

Today we've noticed that the reference track is strangely gone. An error or some planned change in the code?

Thanks!

jrobinso commented 4 years ago

Definitely not planned! I'll look into it.

On Tue, Apr 7, 2020 at 7:34 AM Chiara Rasi notifications@github.com wrote:

Hi @jrobinso https://github.com/jrobinso, we are planning to switch to the new release as soon as it's out, and in the meanwhile we've been using the nightly snapshot (http://igv.org/web/snapshot/dist/igv.js) which contains this bugfix.

Today we've noticed that the reference track is strangely gone. An error or some planned change in the code?

Thanks!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/igvteam/igv.js/issues/1077#issuecomment-610423041, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAHD2HHXIUWF6PD7HKCX7NLRLM2XVANCNFSM4LGPELLA .

jrobinso commented 3 years ago

I think this is resolved, if not re-open a new issue this was has multiple topics.

northwestwitch commented 3 years ago

Yes, it works perfectly now, thanks!!!