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