hakyimlab summary-gwas-imputation issues

hakyimlab / summary-gwas-imputation

harmonization, liftover, and imputation of summary statistics from GWAS

MIT License

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issues

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when merging to snp_reference_metadata ,only 10% snp reserved

#26 Davidseye opened 2 months ago
0
OSError: Couldn't deserialize thrift: TProtocolException: Exceeded size limit

#25 lintingyi2014 opened 6 months ago
0
In the example data on summary statistics imputation, there is a .bed file eur_ld.bed.gz to run per-region imputation. Is summary statistics-based imputation by region applicable only for population-specific GWASes? Are there any ld block schemes applicable to multipopulation studies?

#24 ACDBio opened 9 months ago
0
Error running run_coloc.py : dataset 1: missing required element(s) snp

#23 JieWu2012 opened 9 months ago
1
error when run_coloc.py

#22 JieWu2012 opened 9 months ago
0
AttributeError: 'DataFrame' object has no attribute 'sample_size'

#21 github-wzchhh opened 12 months ago
0
No objects to concatenate in post processing step

#20 hsmith9002 closed 1 year ago
1
Losing almost all variants after restricting to reference step in harmonization.

#19 hsmith9002 closed 1 year ago
2
liftover from hg19 -> hg38

#18 soren-rand closed 1 year ago
7
Script output: gwas_summary_imputation.py

#17 VasoLG opened 2 years ago
1
Imputation error: "AttributeError: type object 'object' has no attribute 'dtype'"

#16 katyaorlova opened 2 years ago
0
Failing harmonization

#15 lauraand1705 closed 3 years ago
0
post-processing of imputed chromosome files

#14 romlindien closed 1 year ago
4
AttributeError("'pyarrow.lib.ChunkedArray' object has no attribute 'name'") when using gwas_summary_imputation.py

#13 DafniG closed 3 years ago
3
Error in gwas harmonization step

#12 rosoffdb closed 3 years ago
1
Coloc with GTEx data: WARNING - R[write to console]: Error in process.dataset(d = dataset1, suffix = " dataset df1: Length of snp names and beta vectors must match

#11 lauraand1705 closed 3 years ago
1
Report "OSError: Invalid flatbuffers message." when reading parquet files.

#10 shuliliu1991 closed 3 years ago
2
ImageXcan-specific changes

#9 meliao closed 4 years ago
0
KeyError: "['zscore'] not in index"

#8 lauraand1705 closed 3 years ago
1
KeyError: "['n_cases'] not in index"

#7 gustavahlberg closed 4 years ago
1
ValueError: invalid literal for int() with base 10: '1_KI270766v1_alt'

#6 carbocation closed 4 years ago
1
Add rsid column arg

#5 jhchung closed 4 years ago
1
Mismatched order of imputation column and header

#4 jhchung closed 4 years ago
1
Output problem with gwas_parsing.py

#3 lauraand1705 closed 4 years ago
5
gtex_v8_eur_filtered.txt.gz

#2 DCousminer closed 4 years ago
10
Create LICENSE.md

#1 Heroico closed 5 years ago
0