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List 1000 Genomes

Command examples:

atav.sh --list-1000-genomes --variant PATH_TO_YOUR_VARIANT_FILE --out PATH_TO_OUTPUT_DIR

Command options:

--list-1000-genomes: trigger list 1000 genomes function.

--variant: use a variant id file (one id per line) or a variant id list (comma delimited)

id format: chr-pos-ref-alt

--1000-genomes-pop: is to specify which population (global, eas, eur, afr, amr or sas) should be used for the 1000 genomes maf cutoff. you can require the cutoff to be met in multiple populations by putting a comma between them, for example --1000-genomes-pop eas,eur,afr.

--max-1000-genomes-maf: specify a maximum 1000 genomes minor allele frequency. (include NA)

Output:

1000_genomes.csv

  • Variant ID
  • 1000 Genomes GLOBAL maf
  • 1000 Genomes EAS maf
  • 1000 Genomes EUR maf
  • 1000 Genomes AFR maf
  • 1000 Genomes AMR maf
  • 1000 Genomes SAS maf

For additional details, please check 1000 Genomes.