Merge branch 'csv---tsv' into 'master'

csv---tsv

See merge request statistical-genetics/jass_suite_pipeline!8

README.md

@@ -62,7 +62,7 @@ See sections below, for running the imputation step and/or the LD-score step.
 
 The following Item are necessary to run JASS pipeline on real data
 
-1. --meta_data: A path toward a meta-data file describing GWAS (see example file in ./input_files/test1.csv and [jass_preprocessing documentation](http://statistical-genetics.pages.pasteur.fr/jass_preprocessing/))
+1. --meta_data: A path toward a meta-data file describing GWAS (see example file in ./input_files/test1.tsv and [jass_preprocessing documentation](http://statistical-genetics.pages.pasteur.fr/jass_preprocessing/))
 2. --gwas_folder: A path toward a folder containing the summary statistics to analyze
 3. --ref_panel_WG: a path toward a reference panel (all genome as 1 file). See below to download curated reference panels by ancestries derived from 1000G V3 on hg38 assembly
 4. --region: Quasi LD independent regions. These regions are used by JASS to determine quickly LD-independent hits accross the genome. The input_files folder contains one region file by ancestry on hg38 assembly. If working with a different assembly or population, you can provide 1Mb delimitations as a rough equivalent of these regions.

input_files/test1.tsv

+filename	internalDataLink	Consortium	Outcome	FullName	Type	Reference	ReferenceLink	dataLink	Nsample	Ncase	Ncontrol	Nsnp	snpid	a1	a2	freq	pval	n	z	OR	se	code	imp	ncas	ncont	altNcas	altNcont	Unnamed: 28
+GIANT_HEIGHT_Wood_et_al_2014_publicrelease_HapMapCeuFreq.txt		GIANT	HEIGHT	Height	Anthropometry	Wood et al. 2014	http://www.ncbi.nlm.nih.gov/pubmed/25282103	https://www.broadinstitute.org/collaboration/giant/index.php/GIANT_consortium_data_files 	253288			2550858.0	MarkerName	Allele1	Allele2	Freq.Allele1.HapMapCEU	p	N	b		SE
+SNP_gwas_mc_merge_nogc.tbl.uniq		GIANT	BMI	Body Mass Index	Anthropometry	Locke et al. 2015	http://www.ncbi.nlm.nih.gov/pubmed/25673413	https://www.broadinstitute.org/collaboration/giant/index.php/GIANT_consortium_data_files 	339224			2554637.0	SNP	A1	A2	Freq1.Hapmap	p	N	b		se