MRCIEU/gwas2vcf

Issues

• error：Variants could not be read

  #83 opened 3 months ago by GGboy-Zzz
  0

• no 'shape' argument in main.py

  #82 opened 3 months ago by GGboy-Zzz
  1

• Does gwas2vcf implementation of multi GWAS storage?

  #81 opened a year ago by nicksunderland
  2

• jsonmeta parameter implementation?

  #80 opened a year ago by nicksunderland
  0

• a dataset processed with gwas2vcf is different from the same dataset preprocessed by Opengwas

  #78 opened 2 years ago by matteofloris
  2

• Same rsID assigned to two different SNPs

  #76 opened 2 years ago by matteofloris
  4

• merge multiple GWAS files

  #70 opened 3 years ago by jielab
  6

• code coverage

  #68 opened 3 years ago by mcgml
  0

• add workflow to mkdocs

  #67 opened 3 years ago by mcgml
  0

• check for the chrom names in the input vs dbSNP & reference fasta

  #63 opened 3 years ago by darked89
  1

• could not read from remote repository

  #64 opened 3 years ago by jielab
  2

• ValueError: fetch requires an index

  #65 opened 3 years ago by jielab
  1

• OSError: error when opening file `human_g1k_v37.fasta.gz`

  #66 opened 3 years ago by jielab
  1

• add citation.cff

  #62 opened 3 years ago by mcgml
  0

• add to pypi

  #61 opened 3 years ago by mcgml
  1

• How to parse GWAS from PMID: 30224653

  #60 opened 3 years ago by vforget
  2

• reference genome base checking

  #58 opened 3 years ago by darked89
  1

• pickle.dump(result, results): no space left on the device

  #59 opened 3 years ago by darked89
  1

• md5 checksums for inputs

  #57 opened 3 years ago by darked89
  0

• benchmarks and speedups

  #56 opened 3 years ago by darked89
  8

• add QC report to docs

  #45 opened 3 years ago by mcgml
  0

• build and push docker images to dockerhub

  #49 opened 3 years ago by mcgml
  0

• update docs

  #39 opened 3 years ago by mcgml
  0

• different naming schemes in dbsnp.v153.b37.vcf.gz vs dbsnp.v153.hg38.vcf.gz

  #54 opened 3 years ago by darked89
  3

• compress fasta files used in example

  #51 opened 3 years ago by darked89
  1

• alias file

  #53 opened 3 years ago by tillandlauer
  1

• No output file

  #50 opened 3 years ago by edwardhumphreys
  12

• inf in estimate field

  #42 opened 3 years ago by mcgml
  0

• Difficulty with --dbsnp/alias

  #48 opened 4 years ago by jinghuazhao
  9

• Sample sizes formatted to only 6 significant digits

  #47 opened 4 years ago by mja
  1

• add chromosome alias option

  #43 opened 4 years ago by mcgml
  0

• host reference genome data

  #44 opened 4 years ago by mcgml
  4

• create flow diagram of operation

  #41 opened 4 years ago by mcgml
  0

• update to new schema

  #40 opened 4 years ago by mcgml
  0

• creating package and app from single repo

  #25 opened 4 years ago by mcgml
  0

• Marshmallow for reading GWAS data

  #19 opened 4 years ago by mcgml
  0

• implement travis ci

  #27 opened 4 years ago by mcgml
  1

• bcftools norm output

  #26 opened 4 years ago by mcgml
  2

• annotate with dbSNP on the fly

  #33 opened 4 years ago by mcgml
  1

• implement variant normalisation

  #32 opened 5 years ago by mcgml
  1

• allow json fields in commandline input

  #34 opened 5 years ago by mcgml
  1

• check binary/continuous flag in vcf files

  #36 opened 5 years ago by mcgml
  0

• implement VR package

  #35 opened 5 years ago by mcgml
  0

• use temp file for processing data rather than mem

  #30 opened 5 years ago by mcgml
  2

• deploy as web app for processing data

  #28 opened 5 years ago by mcgml
  0

• error when no snp col is provided

  #29 opened 5 years ago by mcgml
  1

• move original dbsnp field to INFO

  #24 opened 5 years ago by mcgml
  0

• bgzip or gzip?

  #22 opened 5 years ago by explodecomputer
  5

• should use case and sample size to avoid ambiguity

  #20 opened 5 years ago by mcgml
  0

• add flag for tophits instead of using a new file

  #18 opened 5 years ago by mcgml
  1