lifebit-ai gwas issues - Githubissues

lifebit-ai / gwas

GWAS pipeline using SAIGE

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Chore: Updates template files

#133 CristiGuijarro closed 1 year ago
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REGENIE: cannot read file `*.loco* on CloudOS

#132 evagradovich opened 2 years ago
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{EG} add analysis mode to SAIGE

#131 evagradovich opened 2 years ago
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REGENIE first implementation

#130 evagradovich closed 2 years ago
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BOLT-LMM: Link output to visualizations + report

#129 evagradovich opened 2 years ago
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BOLT-LMM: add docs

#128 evagradovich opened 2 years ago
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Adds BOLT-LMM support

#127 evagradovich closed 2 years ago
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Memory allocation errors in plink when running with larger datasets

#126 evagradovich opened 2 years ago
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For different memory labels, change proportion of RAM assigned to plink

#125 evagradovich opened 2 years ago
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Bgen test config CI tests failing with latest NXF version (21.10.0)

#124 evagradovich opened 2 years ago
1
{EG} add covariate cols

#123 evagradovich closed 2 years ago
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Add bgen support

#122 evagradovich closed 2 years ago
1
Add option to accept genome-wide files as input and split by chromosome

#121 evagradovich opened 2 years ago
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Add support for supplying vcf and indices via --input_folder_location parameter

#120 evagradovich closed 2 years ago
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Support use of only PCs as covariates

#119 evagradovich opened 3 years ago
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Adds PCA step and use of PCs as covariates in SAIGE model fitting step

#118 evagradovich closed 2 years ago
1
Generate and report lambda genomic control inflation factor in report

#117 evagradovich closed 2 years ago
1
Adds docs and extra set of LD pruning steps

#116 cgpu opened 3 years ago
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Replace the s3 bucket with s3://lifebit-featured-datasets

#115 cgpu opened 3 years ago
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Generates plink files for GRM

#114 evagradovich closed 3 years ago
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Implement steps to generate grm_plink_input plink files within the pipeline

#113 evagradovich closed 2 years ago
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Moves docker containers to quay.io

#112 Vlad-Dembrovskyi closed 3 years ago
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Parameterise or deprecate sampleFile

#111 cgpu closed 2 years ago
1
{EG} add standard config

#110 evagradovich closed 3 years ago
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make test configs runnable on CloudOS

#109 evagradovich opened 3 years ago
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{EG} add pheno col parameter

#108 evagradovich closed 3 years ago
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Flexible input for phenotype name

#107 evagradovich closed 2 years ago
2
Implement individual-level missingness filter

#106 evagradovich opened 3 years ago
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Refactoring fixes

#105 evagradovich closed 3 years ago
1
Updates test data

#104 Vlad-Dembrovskyi closed 3 years ago
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Pipeline improvements

#103 Vlad-Dembrovskyi closed 3 years ago
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Update test_binary.config

#102 sk-sahu closed 3 years ago
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Docker image needs to be rebuilt

#101 mcamarad opened 3 years ago
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Decouples phenowrangle and all unnecessary tasks

#100 mcamarad closed 3 years ago
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The plink_grm_input parameter is not used at the moment

#99 cgpu closed 3 years ago
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Extracts samples IDs from vcf files and subset pheno data to match genotypic and phenotypic data

#98 mcamarad closed 3 years ago
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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
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documentation fix- phenofile & pheno_data

#93 kousathanas closed 3 years ago
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Update main.nf

#92 kousathanas closed 3 years ago
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Encoding chromosomes as 'chr1' or '1'

#91 kousathanas opened 3 years ago
1
Decouples simulation from pipeline

#90 mcamarad closed 3 years ago
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Expose to user the name of the column of the cohort column used as unique ID

#89 cgpu closed 3 years ago
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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
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Refactors and prepares for stable release of pipeline

#84 mcamarad closed 3 years ago
0