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List Flanking Sequence

Command examples:

atav.sh --list-flanking-seq --variant PATH_TO_VARIANT_FILE --width $WIDTH --out PATH_TO_OUTPUT_DIR

Command options:

  • --list-flanking-seq: trigger list flanking sequence function.

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

id format: chr-pos-ref-alt

  • --width: input the length of the flanking sequences to be output on each side of the variants.

Output:

  • Variant ID - chr-pos-ref-alt
  • Allele
  • Ref Allele
  • Flanking Sequence