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What's new :

V3.7.0

  • pre release : integration of X chromosome in qc

V3.6.0

  • regenie : GxE available for Reginie
  • regenie : accept categorical values see option covariates_type
  • minor problem whith python when coloumn FID, IID was just int in pheno and str in plink file fixed
  • minor bug gemma with heritability using summary statistics: take account N value and header
  • minor bug fixed when rs id was a dot (was discarded), fixed in meta analyses
  • Add option in meta analysis to heterogenity on metal
  • add script to performed conditional analysis using gcta ``

V3.4.1

  • add option used_pval_z for meta analysis[meta/README.md]
  • format/vcf_in_[bimbam,bgen*,impute2].nf :
  • add option cut_hwe : limit optional for hwe
  • add file ind for impute2
  • saige : update of code for last version of saige, add option saige_imputed_data and saige_impute_method}
  • vcf_in_plink : add option to udpate rs id using database
  • python panda compatibility : minor update
  • singularity/docker image : update for plink1.9 last version
  • format/vcf_in_plink.nf :
    • max_plink_cores_merge, plink_mem_req_merge are now two news parameter can defined memory for merge process
    • bug fixed, work with -resume
  • gcta_bin parameters : change parameter for docker compatibility
  • meta/main.nf : minor change to take account NA in summary statistics for p-value and N
  • parameters check for file : formatdata/format_gwasfile.nf, formatdata/vcf_in_plink.nf

V3.5.0

##V3.4.0

  • finemapping, version 3.3.0 paintor install on docker singularity image, if paintor_bin=0, paintor will be discarded of workflow
  • general :
  • add nextflow.enable.dsl = 1 to all nf script for compatibility new version of nextflow.
  • add control of arguments input of assoc/main.nf, finemapping/main.nf, finemapping/cond-assos.nf, finemapping/finemap_region.nf and meta/main.nf
  • association :
    • add regenie software for association assoc
  • add plink input for saige assoc
  • add bgen support for saige,bolt-lmm and gcta and regenie assoc
  • list_bgen option to complete bgen for saige, regenie and boltlmm in assoc
  • bgen : for one file
  • docker :
  • image docker/singularity of saige : change by official image from github
  • image of rproject : image based by ubuntu 22.04 and R 4.2
  • example :
  • found example and command line of pipeline in h3agwas-examples
  • finemaping :
  • finemapping/finemap_region.nf : 1000 genome downlowd if there is no genetics data
  • finemapping/main.nf : change script of extraction and algoritm for faster and improvment algoritm
  • cut_maf : option work for finemap_region and main [default : 0.01]
  • qc :
  • minor bug fixed for new version of nextflow
  • reorganisation of output

previous change :

  • 2022-06-10 : update meta of metasoft, add column for N, Frequencies for each publication in merge result
  • 2022-05-04 : preprint manuscript can be found on biorxiv
  • 2021-11-04 : association script include saige software
  • 2021-10-25 : new script to do a conditional analysis using gemma see finemapping
  • 2021-09-15 : add for script in finemapping finemap_multi.nf, extract positions using plink, do define independant position in function of minimum p-value and for each independant position apply finemapping finemapping
  • 2021-03-09 : add plot and merge for estimation of heritabilities
  • 2021-03-08 : re organise pipeline :
    • estimation of heritabilities assoc/esth2-assoc.nf move at heritabilites/main.nf
    • do a cojo using gcta : assoc/cojo-assoc.nf move at finemapping/cojo-assoc.nf
    • meta association assoc/meta-assoc.nf move at meta/meta-assoc.nf
    • meta using mtag association assoc/mtag-assoc.nf move at meta/mtag-assoc.nf
    • permutation assoc/permutation-assoc.nf move at utils/permutation/main.nf
    • simulation of phenotype using phenosim assoc/simul-assoc.nf utils/build_example_data/simul-assoc.nf
  • 2021-02-18: add pipeline to build a example data using gwas catalog and 1000 genome build_example_data
  • 2021-02-16: add report to vcf in plink with analyse of frequencies and score formatdata
  • 2021-01-22: create utils folder to add Metasoft binary and utils (server down)
  • 2020-12-08: add meta analyse with plink assoc
  • 2020-12-01: add plink GxE, add estimation of beta and se assoc
  • 2020-11-17: add module nf to convert vcf in bgen format formatdata
  • 2020-07-27: add covariable qualitatif to fastgwa assoc
  • 2020-07-27: News nextflow modules to transform vcf impute format in bimbamformatdata
  • 2020-06-03: News nextflow modules to transform plink file in vcf file with check allele for imputationformatdata
  • 2020-05-18: fixed bug in gcta to computed heribilities assoc
  • 2020-03-27: added a modules to convert position between different genome version formatdata
  • 2020-02-20: support for awsbatch
  • 2020-02-20 : added fastgwa (software gcta) as assoc software : assoc
  • 2019-10-01 : added in transform data a nextflow script to format output of GWAS with added your own rs, frequencies, N etc... (usefull for post analysis) : formatdata
    • file formatdata/format_gwasfile.nf
  • 2019/09/19 : added in estimation of heritabilites option for Multiple variance components for boltlmm assoc
  • 2019/09/17 : added format and analysis by mtag in assoc
  • 2019/09/16 : added two news nextflow files to convert data in formatdata:
    • formatdata/vcf_in_plink.nf : format data in vcf for plink
    • formatdata/vcf_in_impute2.nf : extract impute2 data from vcf of sanger
  • 2019/09/10 : update estimation of heritability in assoc to take account for each software when heritabilities can't be computed