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