README_wits.md

run pipeline to bayes model S tested.

wits pipeline : ''' sumtat=filesumtat if [ ! -f allpos ] then rm -f allpos

Chrom ID GenPos PhysPos A1 A2 A2Freq Index WindStart WindEnd WindSize WindWidth N SamplVar LDsum

for file in ls ../ressource/ukb_50k_bigset_2.8M/*.info do sed '1d' $file | awk '{print $1"\t"$4"\t"$2}' >> allpos done fi ls ../ressource/ukb_50k_bigset_2.8M/.bin > list_bin ls ../ressource/ukb_50k_bigset_2.8M/.info > list_info

#ID CHR POS ALT REF AF_ALT beta.ALT SE P Rsq N_case N_control hchr=CHR;hbp=POS;ha1=ALT;ha2=REF;hrs=ID;hp=P;hbeta=beta.ALT;hse=SE;hn="N_case,N_control";hfreq=AF_ALT #gctb_listld
/home/jeantristan/Cancer/BC_gwas/confluence/confluence/pipeline/main.nf --sumstat $sumstat --sumstat_head_chr $hchr --sumstat_head_bp $hbp --sumstat_head_a1 $ha1 --sumstat_head_a2 $ha2 --sumstat_head_rs $hrs --sumstat_head_pval $hp --sumstat_head_beta $hbeta --sumstat_head_se $hse --sumstat_head_n $hn --sumstat_head_freq $hfreq --update_rsid allpos --gctb_ld_bin list_bin --gctb_ld_info list_info -resume -profile slurmSingularity '''

#run on dna-nexus

see manual here

#connection
dx login or dx login --toker
dx mkdir Aim2_Polygenicity/jeantristan

dx build --nextflow \
  --repository https://github.com/jeantristanb/confluence \
  --destination Aim2_Polygenicity/jeantristan/heritability

command line after connexion

dx ls Aim2_Polygenicity/