quinlan-lab vcf2db issues

quinlan-lab / vcf2db

create a gemini-compatible database from a VCF

MIT License

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issues

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vcf2db does not create genotypes table

#71 ramashka328 opened 1 year ago
1
Issue with PED file

#70 nvnieuwk closed 2 years ago
5
Issue querying db's made with latest cyvcf2

#69 matthdsm opened 2 years ago
0
can't get a working pair of vcf2db - gemini

#68 naumenko-sa opened 2 years ago
2
Cannot parse VEP Mastermind CSQ tags which contains URL

#67 nswh opened 3 years ago
1
Import Funcotator annotated output into GeMINI using vcf2db

#66 sprakashUTH opened 3 years ago
0
Add phase set identifier to gemini db

#65 Bin-Guan closed 3 years ago
0
py3 compatibility fix

#64 matthdsm closed 4 years ago
1
Incrementally push to production level databases

#63 matthdsm closed 4 years ago
2
Differences in impact severity between gemini and vcf2db on vep 'MODIFIER' impact variants

#62 nvteja opened 4 years ago
0
Parse error (with example) on somatic flag

#61 lbeltrame opened 4 years ago
2
Remove superflous (and possibly dangerous) raise statement

#60 lbeltrame closed 2 years ago
1
vcf2db can't handle records that were skipped by vcfanno

#59 lbeltrame opened 5 years ago
1
Allow skipping bad records instead of raising exceptions

#58 lbeltrame opened 5 years ago
3
issue with creating database

#57 atimms opened 5 years ago
9
float() argument must be a string or number, spliceAI overlapping intron problem?

#56 Phillip-a-richmond closed 5 years ago
3
Constraints violation when loading a merged VCF

#55 lbeltrame opened 5 years ago
5
Problem while loading file using vcf2db.

#54 snashraf closed 5 years ago
2
vcf2db error for gatk-haplotype vcf files

#53 ahy1221 closed 5 years ago
4
Why dash symbol is not allowed in sample names?

#52 naumenko-sa opened 5 years ago
1
vcf2db converting string values to float

#51 matthdsm closed 5 years ago
10
adds ensembl_gene_id

#50 naumenko-sa closed 5 years ago
0
citing VCF2DB

#49 Phillip-a-richmond closed 3 years ago
3
vcf2db loads Symbol not Ensembl_gene_id into variant_impacts/gene column

#48 naumenko-sa closed 5 years ago
5
Column type set to VARCHAR(10) despite setting Type=Float in VCF file

#47 marivalen opened 5 years ago
3
ImportError: No module named _snappy_cffi

#46 snashraf opened 5 years ago
16
Add python shebang

#45 matthdsm closed 6 years ago
1
vcf2db not copying all fields from the INFO

#44 jgrady-omico closed 6 years ago
1
Add is_canonical column to gene impacts table.

#43 roryk opened 6 years ago
0
vcf2db cli error

#42 matthdsm closed 6 years ago
27
variant prioritization in variants table

#41 matthdsm closed 5 years ago
0
WARNING: unknown severity

#40 davemcg closed 6 years ago
7
Problem with vct to db conversion

#39 alphahmed18 opened 6 years ago
2
vcf2db without samples

#38 parkesK opened 6 years ago
3
Snappy import/compile failure

#37 Phillip-a-richmond closed 5 years ago
0
Feature requests for VCF2DB compatible with GEMINI built-in tools

#36 Phillip-a-richmond opened 6 years ago
8
Larger file not accepted

#35 marivalen opened 6 years ago
2
Problem creating database from vcf file with custom annotations

#34 marivalen closed 6 years ago
2
parsing AF in CSQ tag

#33 matthdsm closed 6 years ago
3
Error while creating db

#32 matthdsm closed 6 years ago
4
snpEff annotations missing from db

#31 matthdsm closed 6 years ago
3
expand functionality of "--impacts-field" argument

#30 matthdsm closed 7 years ago
12
fixed typo in argument call

#29 matthdsm closed 7 years ago
1
fixed "impacts-field" argument call

#28 matthdsm closed 7 years ago
1
Parsing field names

#27 matthdsm closed 7 years ago
4
using vcf2db with mysql/postgres

#26 matthdsm closed 7 years ago
2
Support more dbNSFP fields annotated by VEP

#25 a113n opened 7 years ago
1
Handle string inputs to AF sanity checking

#24 chapmanb closed 7 years ago
7
Update README.md

#23 leipzig closed 7 years ago
1
Just be aware that sqlite (sqlite3) does not work with AWS EFS drive.

#22 spz1st closed 7 years ago
1