How can I run regenie step 2 for all 22 chromosomes at once? I would like regenie to spit out a single output file with gwas summary stats for all 22 chromosomes if feasible. Thanks

• 

  Anastazie Sedlakova DNAnexus Team

  • 17 March 2022 17:49

  Hello,

  on our GWAS visualization webinar we were showing how you can preprocess regenie output, so that all results are in one file.

   

  Here is example code that you can use:

   

  # Concatenate files, assuming all regenie output files are in one directory

  zcat assoc.c1_diabetes_cc.regenie.gz | head -1 > assoc.all.regenie

  find *.gz  -exec sh -c "zcat {} | tail -n +2 -f " \; >> assoc.all.regenie

   

  # Add `#` to the header

  sed '1 s/./#&/' assoc.all.regenie >  assoc_edit.all.regenie

   

  # Convert file from space to tab-separated

  sed 's/ /\t/g' assoc_edit.all.regenie >  multiple_assoc_edit_tab.all.regenie

   

   

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