Category

Sam/Bam Manipulation


Usage

java -jar picard.jar BaitDesigner TARGET=targets.interval_list DESIGN_NAME=new_baits R=reference_sequence.fasta


Manual

TARGETS (File)    The file with design parameters and targets Required.
DESIGN_NAME (String)    The name of the bait design Required.
REFERENCE_SEQUENCE (File)    The reference sequence fasta file Required.
LEFT_PRIMER (String)    The left amplification primer to prepend to all baits for synthesis Default value: ATCGCACCAGCGTGT. This option can be set to 'null' to clear the default value.
RIGHT_PRIMER (String)    The right amplification primer to prepend to all baits for synthesis Default value: CACTGCGGCTCCTCA. This option can be set to 'null' to clear the default value.
DESIGN_STRATEGY (DesignStrategy)    The design strategy to use to layout baits across each target Default value: FixedOffset. This option can be set to 'null' to clear the default value. Possible values: {CenteredConstrained, FixedOffset, Simple}
BAIT_SIZE (Integer)    The length of each individual bait to design Default value: 120. This option can be set to 'null' to clear the default value.
MINIMUM_BAITS_PER_TARGET (Integer)    The minimum number of baits to design per target. Default value: 2. This option can be set to 'null' to clear the default value.
BAIT_OFFSET (Integer)    The desired offset between the start of one bait and the start of another bait for the same target. Default value: 80. This option can be set to 'null' to clear the default value.
PADDING (Integer)    Pad the input targets by this amount when designing baits. Padding is applied on both sides in this amount. Default value: 0. This option can be set to 'null' to clear the default value.
REPEAT_TOLERANCE (Integer)    Baits that have more than REPEAT_TOLERANCE soft or hard masked bases will not be allowed Default value: 50. This option can be set to 'null' to clear the default value.
POOL_SIZE (Integer)    The size of pools or arrays for synthesis. If no pool files are desired, can be set to 0. Default value: 55000. This option can be set to 'null' to clear the default value.
FILL_POOLS (Boolean)    If true, fill up the pools with alternating fwd and rc copies of all baits. Equal copies of all baits will always be maintained Default value: true. This option can be set to 'null' to clear the default value. Possible values: {true, false}
DESIGN_ON_TARGET_STRAND (Boolean)    If true design baits on the strand of the target feature, if false always design on the + strand of the genome. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
MERGE_NEARBY_TARGETS (Boolean)    If true merge targets that are 'close enough' that designing against a merged target would be more efficient. Default value: true. This option can be set to 'null' to clear the default value. Possible values: {true, false}
OUTPUT_AGILENT_FILES (Boolean)    If true also output .design.txt files per pool with one line per bait sequence Default value: true. This option can be set to 'null' to clear the default value. Possible values: {true, false}
OUTPUT_DIRECTORY (File)    The output directory. If not provided then the DESIGN_NAME will be used as the output directory Default value: null.


Share your experience or ask a question