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macarthur-lab
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clinvar
This repo provides tools to convert ClinVar data into a tab-delimited flat file, and also provides that resulting tab-delimited flat file.
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Bugfix/sap 11534 handle clnhgvs using measure set name
#58
kevin-dunnicliffe
opened
5 years ago
0
missing hgvs_c when indel is realigned and shifted.
#57
sicotte
opened
5 years ago
0
Multiple isoforms not in index
#56
sicotte
opened
5 years ago
0
Add DEPRECATED message
#55
bw2
closed
6 years ago
2
Mismatch between clinical_significance_ordered and submitters_ordered
#54
giladmishne
opened
6 years ago
2
missing clinvar_alleles_with_exac_v1.*.tsv.gz
#53
gpcr
closed
6 years ago
1
Augmented tables in output
#52
balchlab
closed
6 years ago
2
Restore `_ordered` fields handling
#51
kristjaneerik
opened
6 years ago
5
Convert the pipeline to hail for .tsv processing steps?
#50
bw2
opened
6 years ago
0
Update pipeline script
#49
James-CG
closed
7 years ago
0
Clinical Significance Order Lost in Allele Grouping
#48
raymond301
closed
6 years ago
8
License
#47
konradjk
closed
7 years ago
0
ClinSig changes for some halpotypes in join_data.R - become wrong!
#46
raymond301
opened
7 years ago
2
Need to Update pathogenic & conflict boolean regex.
#45
raymond301
closed
7 years ago
1
Add LICENSE
#44
konradjk
closed
7 years ago
2
Another translation for gold stars
#43
raymond301
closed
7 years ago
0
Job parse failure on system execution. ENV issues?
#42
raymond301
closed
6 years ago
5
Fix_Aug2017
#41
XiaoleiZ
closed
7 years ago
2
Improper labelling of conflicting variants as pathogenic
#40
ManavalanG
closed
7 years ago
3
Improper handling of pseudoautosomal region
#39
ManavalanG
closed
7 years ago
1
Add "last_evaluated" field to VCF
#38
bw2
closed
7 years ago
0
Wrong gene mapping
#37
ManavalanG
closed
7 years ago
2
Feature request: Including strand info and genomic start and end coordinates
#36
ManavalanG
closed
7 years ago
1
RScript crash
#35
dashgenomics
closed
7 years ago
1
Fix multi allele parsing
#34
XiaoleiZ
closed
7 years ago
1
[WIP] Propagating ordered fields
#33
kristjaneerik
closed
7 years ago
11
Missing variants
#32
bcrone
opened
7 years ago
4
Sometimes "symbol" disagrees with primary hgvs gene annotation
#31
simnim
closed
7 years ago
1
generate clinvar_alleles_with_gnomad table(s)
#30
bw2
closed
7 years ago
4
should code be moved to a separate github repo from the data?
#29
bw2
closed
7 years ago
4
Add 2 new columns to retain the clinical significances and review statuses from each submitter.
#28
raymond301
closed
7 years ago
1
add .gitignore File to Repo?
#27
raymond301
closed
7 years ago
2
Semi-colon in pathogenic, benign and conflicted columns. Bug?
#26
ManavalanG
closed
7 years ago
1
List Order Mismatch between Clinical_Sig & All_Summiters
#25
raymond301
closed
7 years ago
1
Add GRCh38 support (fixes #22) and update to Feb 2. clinvar release
#24
bw2
closed
7 years ago
0
Creat variant conditions record
#23
XiaoleiZ
closed
7 years ago
0
b38 availability?
#22
gpcr
closed
7 years ago
3
Parsing the relevant info from XML
#21
XiaoleiZ
closed
7 years ago
1
Missing data issue
#20
peterzt
closed
7 years ago
4
Issue with R script
#19
VivekTodur
closed
7 years ago
3
Fix incorrect ExAC parsing and enable using older ClinVar data
#18
kristjaneerik
closed
8 years ago
1
Something wrong?
#17
ryuzheng
closed
8 years ago
0
Move output files to base dir
#16
bw2
closed
8 years ago
0
Request: Adding Benign column to the output
#15
vigneshravi
closed
8 years ago
7
Fixes #13: correct input file for join_data.R
#14
roland-ewald
closed
8 years ago
2
join_data.R fails because of input file not being found
#13
roland-ewald
closed
8 years ago
0
Added inheritance_modes and other new columns. Closes #11.
#12
bw2
closed
8 years ago
0
I would like to have the ModeOfInheritence field in the flatfile.
#11
vigneshravi
closed
8 years ago
7
Origin column
#10
sigven
closed
8 years ago
3
Update?
#9
sigven
closed
8 years ago
1
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