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lifebit-ai
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gwas
GWAS pipeline using SAIGE
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Chore: Updates template files
#133
CristiGuijarro
closed
1 year ago
0
REGENIE: cannot read file `*.loco* on CloudOS
#132
evagradovich
opened
2 years ago
0
{EG} add analysis mode to SAIGE
#131
evagradovich
opened
2 years ago
0
REGENIE first implementation
#130
evagradovich
closed
2 years ago
0
BOLT-LMM: Link output to visualizations + report
#129
evagradovich
opened
2 years ago
0
BOLT-LMM: add docs
#128
evagradovich
opened
2 years ago
0
Adds BOLT-LMM support
#127
evagradovich
closed
2 years ago
0
Memory allocation errors in plink when running with larger datasets
#126
evagradovich
opened
3 years ago
0
For different memory labels, change proportion of RAM assigned to plink
#125
evagradovich
opened
3 years ago
0
Bgen test config CI tests failing with latest NXF version (21.10.0)
#124
evagradovich
opened
3 years ago
1
{EG} add covariate cols
#123
evagradovich
closed
3 years ago
0
Add bgen support
#122
evagradovich
closed
3 years ago
1
Add option to accept genome-wide files as input and split by chromosome
#121
evagradovich
opened
3 years ago
0
Add support for supplying vcf and indices via --input_folder_location parameter
#120
evagradovich
closed
3 years ago
0
Support use of only PCs as covariates
#119
evagradovich
opened
3 years ago
0
Adds PCA step and use of PCs as covariates in SAIGE model fitting step
#118
evagradovich
closed
3 years ago
1
Generate and report lambda genomic control inflation factor in report
#117
evagradovich
closed
3 years ago
1
Adds docs and extra set of LD pruning steps
#116
cgpu
opened
3 years ago
0
Replace the s3 bucket with s3://lifebit-featured-datasets
#115
cgpu
opened
3 years ago
0
Generates plink files for GRM
#114
evagradovich
closed
3 years ago
0
Implement steps to generate grm_plink_input plink files within the pipeline
#113
evagradovich
closed
3 years ago
0
Moves docker containers to quay.io
#112
Vlad-Dembrovskyi
closed
3 years ago
0
Parameterise or deprecate sampleFile
#111
cgpu
closed
3 years ago
1
{EG} add standard config
#110
evagradovich
closed
3 years ago
0
make test configs runnable on CloudOS
#109
evagradovich
opened
3 years ago
0
{EG} add pheno col parameter
#108
evagradovich
closed
3 years ago
0
Flexible input for phenotype name
#107
evagradovich
closed
3 years ago
2
Implement individual-level missingness filter
#106
evagradovich
opened
3 years ago
0
Refactoring fixes
#105
evagradovich
closed
3 years ago
1
Updates test data
#104
Vlad-Dembrovskyi
closed
3 years ago
0
Pipeline improvements
#103
Vlad-Dembrovskyi
closed
3 years ago
0
Update test_binary.config
#102
sk-sahu
closed
3 years ago
0
Docker image needs to be rebuilt
#101
mcamarad
opened
3 years ago
0
Decouples phenowrangle and all unnecessary tasks
#100
mcamarad
closed
3 years ago
0
The plink_grm_input parameter is not used at the moment
#99
cgpu
closed
3 years ago
0
Extracts samples IDs from vcf files and subset pheno data to match genotypic and phenotypic data
#98
mcamarad
closed
3 years ago
0
Replace duplicate gwas_1_fit_null_glmm by refactoring (expose traitType, invNormalize )
#97
cgpu
closed
3 years ago
1
Side by side comparison of gwas_filtering_bin vs gwas_filtering_qt: Why do we need 2 different processes?
#96
cgpu
closed
3 years ago
1
Debugging refactoring
#95
cgpu
closed
3 years ago
0
Update SAIGE version to latest
#94
kousathanas
opened
3 years ago
0
documentation fix- phenofile & pheno_data
#93
kousathanas
closed
3 years ago
0
Update main.nf
#92
kousathanas
closed
3 years ago
0
Encoding chromosomes as 'chr1' or '1'
#91
kousathanas
opened
3 years ago
1
Decouples simulation from pipeline
#90
mcamarad
closed
3 years ago
0
Expose to user the name of the column of the cohort column used as unique ID
#89
cgpu
closed
3 years ago
0
Hardcoded sampleFile name in step2_SPAtests.R
#88
cgpu
closed
3 years ago
2
Error when running gel-gwas with simulated data related to inconsistent number of participants between the pheno file and the VCF file
#87
mmeier93
closed
3 years ago
1
Query fails to join query dictionary with the pheno metadata
#86
mcamarad
closed
3 years ago
0
Differing number of rows after transformation while testing with covid cohort
#85
mcamarad
closed
3 years ago
0
Refactors and prepares for stable release of pipeline
#84
mcamarad
closed
4 years ago
0
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