lifebit-ai simulate issues

lifebit-ai / simulate

Simulate genomic data on demand

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Simulate ancestry admixture using 1000Genomes haplotypes

#57 evagradovich opened 3 years ago
0
using neutral params

#56 mmeier93 closed 3 years ago
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Add merging of plink files to match GRM plink input

#55 mcamarad opened 3 years ago
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Immplements sample_ids and reheader vcf

#54 cgpu opened 3 years ago
0
Add option to use a samples_id.txt file instead of num of participants

#53 cgpu opened 3 years ago
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Add ability to handle/produce different leg files (i.e. different number of SNPs)

#52 mmeier93 opened 3 years ago
0
Refactors hapgen simulation step to correct awk bug and allow simulation of >40,000 individuals

#51 mmeier93 closed 3 years ago
1
Adds extra refinements (N cases to proportion (0,1) ~ N sample size)

#50 mmeier93 opened 3 years ago
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Decide how to handle mininum and maximum number of cases needed by GTCA

#49 mmeier93 opened 3 years ago
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Refactors --gwas_cases (and removes --gwas_controls) to allow proportion of cases to be supplied by user

#48 mmeier93 closed 3 years ago
1
Is this process needed or could we repurpose the one for the --simulate_vcf?

#47 cgpu opened 3 years ago
0
Check if bcftools query can retrieve sample ids from binary plink files

#46 cgpu opened 3 years ago
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Use variables in input directive instead of strings

#45 cgpu opened 3 years ago
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fastNGSadmix/data1000genomes.tar.gz

#44 cgpu opened 3 years ago
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Unstable behaviour when running pipeline on CloudOS

#43 mcamarad opened 3 years ago
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Perfect the summary[] in main.nf to clarify exactly which params were provided

#42 mmeier93 opened 3 years ago
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Remove remaining nf-core template related params

#41 mmeier93 opened 3 years ago
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Can we scatter even further, beyond chromosomes and have smaller and more regions?

#40 cgpu opened 3 years ago
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Change gwas_case, gwas_controls and keep cases_proportion relative to N sample size

#39 cgpu closed 3 years ago
1
Add number of participants in log or encode in filename

#38 cgpu opened 3 years ago
0
Extract sample ids from genomic files (vcf, plink)

#37 mcamarad closed 2 years ago
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sample IDs from plink files do not match ones from vcfs.

#36 mcamarad opened 3 years ago
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Expands simulate pheno with query.json and metadata files

#35 mcamarad closed 3 years ago
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PR for adding more additional ci testing

#34 mmeier93 closed 3 years ago
1
Add pheno_col entry in sim_config YAML and add attribute of pheno_col entry named `fraction_of_cases`

#33 mcamarad closed 3 years ago
0
Create generate_sim_config.R script, given the json query and pheno metadata to extract from exported cohort a config file with required fields for using with simulate_pheno_data.R

#32 mcamarad closed 3 years ago
0
Decouple distro params values required for sim_conf.yml from infer them from query json and pheno metadata file and create a YAML that generalises for all categories of data

#31 mcamarad closed 3 years ago
0
PR to add comments to clarify how one should interpret the GCTA output

#30 mmeier93 closed 4 years ago
1
PR to add additional CI testing

#29 mmeier93 closed 4 years ago
3
Add detailed documentation on the simulate_cb_output_config.yml

#28 mmeier93 opened 4 years ago
0
Expose column ID as parameter for users

#27 mcamarad opened 4 years ago
0
PR adding lifebit-ai/gel-gwas pheno simulation scripts

#26 mmeier93 closed 4 years ago
1
VCF files should retain the vcf suffix

#25 cgpu closed 4 years ago
1
PR to add extra VCF formatting steps (compression + indexing) as well as correct CI testing

#24 mmeier93 closed 4 years ago
1
Add CI test data to Lifebit's S3

#23 mmeier93 closed 4 years ago
1
PR to improve extra flag handling, improve download steps and add CI testing

#22 mmeier93 closed 4 years ago
1
Add latest version of all_leg.tar.gz to Lifebit's S3

#21 mmeier93 closed 4 years ago
1
GTCA: determine why number of cases and controls different between input and output

#20 mmeier93 closed 4 years ago
1
Sort out error 141 occuring when running GTCA

#19 mmeier93 opened 4 years ago
0
Modify --effective_population_size

#18 mmeier93 opened 4 years ago
1
Clean up how files/folders are decompressed in place

#17 mmeier93 closed 4 years ago
1
Clarify name of --gwas_quantitative GWAS option

#16 mmeier93 closed 4 years ago
1
Refactor to utilise Nextflow's staging of files power and omit wget

#15 cgpu closed 4 years ago
1
Add information for behaviour when default is updated

#14 cgpu opened 4 years ago
1
PR to add the ability to handle extra options and create summary statistics (GCTA)

#13 mmeier93 closed 4 years ago
1
Sort out extra flag handling (hapgen2 vs GTCA vs METAL)

#12 mmeier93 closed 4 years ago
1
Add a check to ensure gwas cases and gwas controls = num_participantsn+ clarify their description

#11 mmeier93 closed 4 years ago
1
Sort out conversion from .gen to PLINK and VCF

#10 mmeier93 closed 4 years ago
1
GCTA: decide if all files can be input together (and hence if only single list of causal SNPs) is possible

#9 mmeier93 opened 4 years ago
0
GTCA: decide/attempt using .gen and .sample instead of PLINK files as input

#8 mmeier93 opened 4 years ago
0