Command-line endpoints

Below is a list of all the command line endpoints installed with the python package, bash scripts that are available in the gwas_norm/resources/bin directory and task gwas_norm/resources/tasks scripts that were used in job array submissions using the hpc-tools package. Many of these are mentioned in their respective context throughout the documentation but they are listed here all in a single place.

• Python endpoints
  • Core scripts
  • Mapping file generation
    • dbsnp-download
      • Positional Arguments
      • Named Arguments
    • format-dbsnp
      • Positional Arguments
      • Named Arguments
      • Input VCF
      • Output VCF
    • format-alfa
      • Positional Arguments
      • Named Arguments
      • Input VCF
      • Output VCF
    • format-snpstats
      • Positional Arguments
      • Named Arguments
    • fix-vcf-allele-number
      • Named Arguments
    • quick-lift
    • merge-count-vcfs
      • Positional Arguments
      • Named Arguments
    • make-site-chunks
      • Positional Arguments
      • Named Arguments
    • merge-cadd
      • Positional Arguments
      • Named Arguments
    • split-mapping-file
      • Positional Arguments
      • Named Arguments
  • Other admin scripts
    • convert-xml
      • Positional Arguments
      • Named Arguments
    • gwas-norm-test-data
      • Positional Arguments
      • Named Arguments
      • Test config file
• BASH endpoints
  • Mapping file generation
    • process-dbsnp.sh
      • Unwanted INFO fields
      • Input vcf
      • Output VCF
    • process-alfa.sh
      • Input vcf
      • Output VCF
    • process-gnomad2.sh
    • process-gnomad3.sh
    • process-1000g.sh
    • process-snpstats.sh
    • vcf-lift.sh
      • Example usage
    • vcf-sort.sh
    • vcf-cat.sh
    • vcf-dumb-cat.sh
    • merge-count-vcfs.sh
    • make-vep-ja.sh
      • Example usage