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# Annotation pipeline : `annotation/main.nf`

This section describes a pipeline in devlopment, purpose of this pipeline is to extract, plot of specific position from gwas result, phenotype and genotype, and annotate positoin

Main option

The key options are:

  • work_dir : the directory in which you will run the workflow. This will typically be the h3agwas directory which you cloned
  • output_dir : output directory
  • output : output pattern
  • data : same option that assoc/main.nf, your file of phenotype and covariable
  • pheno : phenotype, must be in data file
  • cov : covariable, if not null must be in data
  • input_pat : the base of set of PLINK bed,bim and fam files (this should only match one);
  • input_dir : the directory of set of PLINK bed,bim and fam files (this should only match one);
  • file_gwas : file contains gwas result, if N or frequencies is not available, it is computed with plink file and data file, to change format header must be defined :
  • head_pval : pvalue header [ default : "P_BOLT_LMM" ]
  • head_freq : freq header [ default : None], if not present computed with plink, (and data/pheno if present)
  • head_n : N (individuals number) [ default : None ], if not present computed with plink (and data/pheno if present)
  • head_rs : rs header column [default : "SNP"]
  • head_beta : beta header colum [default : "BETA"]
  • head_se : column for standard error of beta "SE"
  • head_A1 : column for A0 [default : "ALLELE0" ]
  • head_A2 : column for A1 [default : "ALLELE1" ]
  • list_rs :
  • list of rs where want an analyse, same name of rs must be present in gwas file
  • Annotation :
  • file_annotation :
  • file contains list file by chromosome with information for annotation
  • todescribe
  • info_annotation :
  • give information for each annotation
  • to described
  • locuszoom :
  • loczm_buid : locus zoom build (default hg19)
  • loczm_pop : population of locus zoom
  • loczm_source : source of locus zoom
  • loczm_gwascat : [defaut : none ]
  • loczm_bin : binary of locus zoom, used to defined also database

Installation

  • locuszoom, R : (ggplot2), python3

Example

warning :

aws : locus zoom doesn't work with amazon aws, your must install your own locus zoom and if you need used singularity

command lines

input :

  • plink file
  • summary statistisc
  • phenotype and data file
  • rs from gwas (one or more, separate with comma)
  • Annotation used annovar file, if you don't list_file_annot and info_file_annot, data will be downloaded
## your locus zoom directory 
DirLZ=locuszoom
nextflow run  h3abionet/h3agwas/utils/annotation/main.nf --head_pval p_wald --head_bp ps --head_chr chr --head_rs rs --head_beta beta --head_se se --head_A1 allele1 --head_A2 allele0 --input_dir data/imputed/  --input_pat imput_data --file_gwas data/summarystat/all_pheno.gemma  --output_dir annotation --list_rs "2:45832137:A:G,1:117539108:G:T" --data data/pheno/pheno_test.all --pheno pheno_qt1  -resume  -profile slurmSingularity --loczm_bin  $DirLZ