quinlan-lab / vcf2db

create a gemini-compatible database from a VCF

quinlan-lab/vcf2db Issues

vcf2db does not create genotypes table
Updated a year ago1
Issue with PED file
Closed 2 years ago5
Issue querying db's made with latest cyvcf2
Updated 2 years ago
can't get a working pair of vcf2db - gemini
Updated 2 years ago2
Add phase set identifier to gemini db
Closed 3 years ago
Cannot parse VEP Mastermind CSQ tags which contains URL
Updated 3 years ago1
citing VCF2DB
Closed 3 years ago3
issue with creating database
Updated 3 years ago9
Import Funcotator annotated output into GeMINI using vcf2db
Updated 4 years ago
Why dash symbol is not allowed in sample names?
Updated 4 years ago1
Incrementally push to production level databases
Closed 5 years ago2
Differences in impact severity between gemini and vcf2db on vep 'MODIFIER' impact variants
Updated 5 years ago
Parse error (with example) on somatic flag
Updated 5 years ago2
vcf2db can't handle records that were skipped by vcfanno
Updated 5 years ago1
Allow skipping bad records instead of raising exceptions
Updated 5 years ago3
variant prioritization in variants table
Closed 5 years ago
ImportError: No module named _snappy_cffi
Updated 5 years ago16
float() argument must be a string or number, spliceAI overlapping intron problem?
Closed 5 years ago3
Constraints violation when loading a merged VCF
Updated 5 years ago5
feature request - parallelization
Closed 5 years ago4
Problem while loading file using vcf2db.
Closed 5 years ago2
Ability to add variants to existing database without overwriting
Updated 5 years ago1
vcf2db converting string values to float
Closed 6 years ago10
vcf2db error for gatk-haplotype vcf files
Closed 6 years ago4
vcf2db loads Symbol not Ensembl_gene_id into variant_impacts/gene column
Closed 6 years ago5
Column type set to VARCHAR(10) despite setting Type=Float in VCF file
Updated 6 years ago3
Feature requests for VCF2DB compatible with GEMINI built-in tools
Updated 6 years ago8
Snappy import/compile failure
Closed 6 years ago
vcf2db cli error
Closed 6 years ago27
vcf2db not copying all fields from the INFO
Closed 6 years ago1
snpEff annotations missing from db
Closed 6 years ago3
WARNING: unknown severity
Closed 6 years ago7
vcf2db without samples
Updated 6 years ago3
Problem with vct to db conversion
Updated 6 years ago2
Including extra fields in VEP CSQ tag
Closed 6 years ago8
fill sample_genotype_counts table
Closed 6 years ago6
parsing AF in CSQ tag
Closed 6 years ago3
Problem creating database from vcf file with custom annotations
Closed 6 years ago2
Larger file not accepted
Updated 7 years ago2
Error while creating db
Closed 7 years ago4
expand functionality of "--impacts-field" argument
Closed 7 years ago12
Parsing field names
Closed 7 years ago4
using vcf2db with mysql/postgres
Closed 7 years ago2
Just be aware that sqlite (sqlite3) does not work with AWS EFS drive.
Closed 7 years ago1
TypeError: ufunc 'isnan' not supported for the input types, and the inputs could not be safely coerced to any supported types according to the casting rule ''safe''
Closed 7 years ago10
Codons are blank?
Closed 7 years ago5
unicode not supported?
Closed 7 years ago8
gene_summary and gene_detailed in Gemini
Updated 8 years ago2
skipping 'AC' because it has Number=A
Closed 8 years ago4
Multiple floats in INFO columns
Closed 8 years ago9