Subsets intervals from a reference sequence to a new FASTA file.This tool takes a list of intervals, reads the corresponding subsquences from a reference FASTA file and writes them to a new FASTA file as separate records. Note that the reference FASTA file must be accompanied by an index file and the interval list must be provided in Picard list format. The names provided for the intervals will be used to name the corresponding records in the output file.
java -jar picard.jar ExtractSequences INTERVAL_LIST=regions_of_interest.interval_list R=reference.fasta O=extracted_IL_sequences.fasta
INTERVAL_LIST (File) Interval list describing intervals to be extracted from the reference sequence. Required.
REFERENCE_SEQUENCE (File) Reference sequence FASTA file. Required.
OUTPUT (File) Output FASTA file. Required.
LINE_LENGTH (Integer) Maximum line length for sequence data. Default value: 80. This option can be set to 'null' to clear the default value.