NAME - Get nucleotde and amino acid sequences from BED intervals

SYNOPSIS [--bed FILE] [--fa FILE] [--aa] [options]


Extract sequence intervals from Fasta files, provided as BED6 records. Optionally translate nucleotide into amino acid sequences. Output is written to a 'sequence.fa' output file. This can be overriden with the -s switch, which triggers STDOUT output.



Input file in BED6 format (mandatory)


Input file in Fasta format (mandatory)


Translate nucleotide into amino acid sequences, providing all three possible frames


Write output to STDOUT instead of an output file 'sequence.fa'

--help -h

Print short help


Prints the manual page and exits


Michael T. Wolfinger <>