MRCIEU gwas2vcf issues - Githubissues

MRCIEU / gwas2vcf

Convert GWAS summary statistics to VCF

MIT License

47 stars 18 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

annotate with dbSNP on the fly

#33 mcgml closed 4 years ago
1
implement variant normalisation

#32 mcgml closed 4 years ago
1
Memory improvements

#31 mcgml closed 4 years ago
2
use temp file for processing data rather than mem

#30 mcgml closed 4 years ago
2
error when no snp col is provided

#29 mcgml closed 4 years ago
1
deploy as web app for processing data

#28 mcgml closed 4 years ago
0
implement travis ci

#27 mcgml closed 4 years ago
1
bcftools norm output

#26 mcgml closed 4 years ago
2
creating package and app from single repo

#25 mcgml closed 4 years ago
0
move original dbsnp field to INFO

#24 mcgml closed 5 years ago
0
changing default to index with tbi and adding option to use csi

#23 explodecomputer closed 5 years ago
1
bgzip or gzip?

#22 explodecomputer closed 5 years ago
5
Sample fields

#21 mcgml closed 5 years ago
0
should use case and sample size to avoid ambiguity

#20 mcgml opened 5 years ago
0
Marshmallow for reading GWAS data

#19 mcgml closed 4 years ago
0
add flag for tophits instead of using a new file

#18 mcgml closed 5 years ago
1
Do not use empty fields, instead do not emit keys

#17 mcgml closed 5 years ago
0
Use absolute number of cases instead of fraction to avoid loss of precision

#16 mcgml closed 5 years ago
0
allow for storing multiple traits per VCF (use the sample field)

#15 mcgml closed 5 years ago
19
Update documentation for running on HPC and Docker

#14 mcgml closed 5 years ago
1
vcf spec 4.3 supports inf; use this for -log10 p instead of 999

#13 mcgml closed 5 years ago
2
case control header set wrong when cohort fraction used

#12 mcgml closed 5 years ago
1
check position is positive integer

#11 mcgml closed 5 years ago
2
check chromosome is in FAI

#10 mcgml closed 5 years ago
2
Wdl

#9 mcgml closed 5 years ago
0
VCF cannot store floats < 1e-6

#8 mcgml closed 5 years ago
15
dealing with non-hg19

#7 mcgml closed 4 years ago
0
For simplicity should we split multi-allelic variants in bcf files?

#6 explodecomputer closed 5 years ago
0
Containerising

#5 explodecomputer closed 5 years ago
0
see spec - mr-base-structure

#4 mcgml closed 5 years ago
2
add PROPCASE for bcf

#3 mcgml closed 5 years ago
0
add static value for sample size and CC

#2 mcgml closed 5 years ago
0
read from zip/gzip/compressed text GWAS

#1 mcgml closed 5 years ago
0