Used in: gor only


The SEQ command returns the corresponding reference sequence read for each row of the output based on the position column.

Other columns can be used instead of the position column (#2) using the -c option. The length of the flanking sequence (the number of bases on either side of the position defaults to 10, but can be changed using the -l option.


gor file | SEQ [ attributes ]


-c cols

The columns for which the reference sequence is found. By default, only column number 2 is used.

-l number

The length of the flanking sequence, e.g. total seq. length is equal to 2*l + 1.