Designs oligonucleotide baits for hybrid selection reactions.
This tool is used to design custom bait sets for hybrid selection experiments. The following files are input into BaitDesigner: a (TARGET) interval list indicating the sequences of interest, e.g. exons with their respective coordinates, a reference sequence, and a unique identifier string (DESIGN_NAME).
The tool will output interval_list files of both bait and target sequences as well as the actual bait sequences in FastA format. At least two baits are output for each target sequence, with greater numbers for larger intervals. Although the default values for both bait size (120 bases) nd offsets (80 bases) are suitable for most applications, these values can be customized. Offsets represent the distance between sequential baits on a contiguous stretch of target DNA sequence.
The tool will also output a pooled set of 55,000 (default) oligonucleotides representing all of the baits redundantly. This redundancy achieves a uniform concentration of oligonucleotides for synthesis by a vendor as well as equal numbersof each bait to prevent bias during the hybrid selection reaction.
Usage example:
java -jar picard.jar BaitDesigner \
TARGET=targets.interval_list \
DESIGN_NAME=new_baits \
R=reference_sequence.fasta
Category Reference
Overview
Designs baits for hybrid selection!BaitDesigner (Picard) specific arguments
This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.
Argument name(s) | Default value | Summary | |
---|---|---|---|
Required Arguments | |||
--DESIGN_NAME |
The name of the bait design | ||
--REFERENCE_SEQUENCE -R |
Reference sequence file. | ||
--TARGETS -T |
The file with design parameters and targets | ||
Optional Tool Arguments | |||
--arguments_file |
read one or more arguments files and add them to the command line | ||
--BAIT_OFFSET |
80 | The desired offset between the start of one bait and the start of another bait for the same target. | |
--BAIT_SIZE |
120 | The length of each individual bait to design | |
--DESIGN_ON_TARGET_STRAND |
false | If true design baits on the strand of the target feature, if false always design on the + strand of the genome. | |
--DESIGN_STRATEGY |
FixedOffset | The design strategy to use to layout baits across each target | |
--FILL_POOLS |
true | If true, fill up the pools with alternating fwd and rc copies of all baits. Equal copies of all baits will always be maintained | |
--help -h |
false | display the help message | |
--LEFT_PRIMER |
ATCGCACCAGCGTGT | The left amplification primer to prepend to all baits for synthesis | |
--MERGE_NEARBY_TARGETS |
true | If true merge targets that are 'close enough' that designing against a merged target would be more efficient. | |
--MINIMUM_BAITS_PER_TARGET |
2 | The minimum number of baits to design per target. | |
--OUTPUT_AGILENT_FILES |
true | If true also output .design.txt files per pool with one line per bait sequence | |
--OUTPUT_DIRECTORY -O |
The output directory. If not provided then the DESIGN_NAME will be used as the output directory | ||
--PADDING |
0 | Pad the input targets by this amount when designing baits. Padding is applied on both sides in this amount. | |
--POOL_SIZE |
55000 | The size of pools or arrays for synthesis. If no pool files are desired, can be set to 0. | |
--REPEAT_TOLERANCE |
50 | Baits that have more than REPEAT_TOLERANCE soft or hard masked bases will not be allowed | |
--RIGHT_PRIMER |
CACTGCGGCTCCTCA | The right amplification primer to prepend to all baits for synthesis | |
--version |
false | display the version number for this tool | |
Optional Common Arguments | |||
--COMPRESSION_LEVEL |
5 | Compression level for all compressed files created (e.g. BAM and VCF). | |
--CREATE_INDEX |
false | Whether to create an index when writing VCF or coordinate sorted BAM output. | |
--CREATE_MD5_FILE |
false | Whether to create an MD5 digest for any BAM or FASTQ files created. | |
--GA4GH_CLIENT_SECRETS |
client_secrets.json | Google Genomics API client_secrets.json file path. | |
--MAX_RECORDS_IN_RAM |
500000 | When writing files that need to be sorted, this will specify the number of records stored in RAM before spilling to disk. Increasing this number reduces the number of file handles needed to sort the file, and increases the amount of RAM needed. | |
--QUIET |
false | Whether to suppress job-summary info on System.err. | |
--TMP_DIR |
One or more directories with space available to be used by this program for temporary storage of working files | ||
--USE_JDK_DEFLATER -use_jdk_deflater |
false | Use the JDK Deflater instead of the Intel Deflater for writing compressed output | |
--USE_JDK_INFLATER -use_jdk_inflater |
false | Use the JDK Inflater instead of the Intel Inflater for reading compressed input | |
--VALIDATION_STRINGENCY |
STRICT | Validation stringency for all SAM files read by this program. Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded. | |
--VERBOSITY |
INFO | Control verbosity of logging. | |
Advanced Arguments | |||
--showHidden |
false | display hidden arguments |
Argument details
Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above.
--arguments_file
read one or more arguments files and add them to the command line
List[File] []
--BAIT_OFFSET
The desired offset between the start of one bait and the start of another bait for the same target.
int 80 [ [ -∞ ∞ ] ]
--BAIT_SIZE
The length of each individual bait to design
int 120 [ [ -∞ ∞ ] ]
--COMPRESSION_LEVEL
Compression level for all compressed files created (e.g. BAM and VCF).
int 5 [ [ -∞ ∞ ] ]
--CREATE_INDEX
Whether to create an index when writing VCF or coordinate sorted BAM output.
Boolean false
--CREATE_MD5_FILE
Whether to create an MD5 digest for any BAM or FASTQ files created.
boolean false
--DESIGN_NAME
The name of the bait design
R String null
--DESIGN_ON_TARGET_STRAND
If true design baits on the strand of the target feature, if false always design on the + strand of the genome.
boolean false
--DESIGN_STRATEGY
The design strategy to use to layout baits across each target
The --DESIGN_STRATEGY argument is an enumerated type (DesignStrategy), which can have one of the following values:
- CenteredConstrained
- Implementation that "constrains" baits to be within the target region when possible.
- FixedOffset
- Design that places baits at fixed offsets over targets, allowing them to hang off the ends as dictated by the target size and offset.
- Simple
- Ultra simple bait design algorithm that just lays down baits starting at the target start position until either the bait start runs off the end of the target or the bait would run off the sequence
DesignStrategy FixedOffset
--FILL_POOLS
If true, fill up the pools with alternating fwd and rc copies of all baits. Equal copies of all baits will always be maintained
boolean true
--GA4GH_CLIENT_SECRETS
Google Genomics API client_secrets.json file path.
String client_secrets.json
--help / -h
display the help message
boolean false
--LEFT_PRIMER
The left amplification primer to prepend to all baits for synthesis
String ATCGCACCAGCGTGT
--MAX_RECORDS_IN_RAM
When writing files that need to be sorted, this will specify the number of records stored in RAM before spilling to disk. Increasing this number reduces the number of file handles needed to sort the file, and increases the amount of RAM needed.
Integer 500000 [ [ -∞ ∞ ] ]
--MERGE_NEARBY_TARGETS
If true merge targets that are 'close enough' that designing against a merged target would be more efficient.
boolean true
--MINIMUM_BAITS_PER_TARGET
The minimum number of baits to design per target.
int 2 [ [ -∞ ∞ ] ]
--OUTPUT_AGILENT_FILES
If true also output .design.txt files per pool with one line per bait sequence
boolean true
--OUTPUT_DIRECTORY / -O
The output directory. If not provided then the DESIGN_NAME will be used as the output directory
File null
--PADDING
Pad the input targets by this amount when designing baits. Padding is applied on both sides in this amount.
int 0 [ [ -∞ ∞ ] ]
--POOL_SIZE
The size of pools or arrays for synthesis. If no pool files are desired, can be set to 0.
int 55000 [ [ -∞ ∞ ] ]
--QUIET
Whether to suppress job-summary info on System.err.
Boolean false
--REFERENCE_SEQUENCE / -R
Reference sequence file.
R File null
--REPEAT_TOLERANCE
Baits that have more than REPEAT_TOLERANCE soft or hard masked bases will not be allowed
int 50 [ [ -∞ ∞ ] ]
--RIGHT_PRIMER
The right amplification primer to prepend to all baits for synthesis
String CACTGCGGCTCCTCA
--showHidden / -showHidden
display hidden arguments
boolean false
--TARGETS / -T
The file with design parameters and targets
R File null
--TMP_DIR
One or more directories with space available to be used by this program for temporary storage of working files
List[File] []
--USE_JDK_DEFLATER / -use_jdk_deflater
Use the JDK Deflater instead of the Intel Deflater for writing compressed output
Boolean false
--USE_JDK_INFLATER / -use_jdk_inflater
Use the JDK Inflater instead of the Intel Inflater for reading compressed input
Boolean false
--VALIDATION_STRINGENCY
Validation stringency for all SAM files read by this program. Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.
The --VALIDATION_STRINGENCY argument is an enumerated type (ValidationStringency), which can have one of the following values:
- STRICT
- LENIENT
- SILENT
ValidationStringency STRICT
--VERBOSITY
Control verbosity of logging.
The --VERBOSITY argument is an enumerated type (LogLevel), which can have one of the following values:
- ERROR
- WARNING
- INFO
- DEBUG
LogLevel INFO
--version
display the version number for this tool
boolean false
GATK version 4.2.4.1-SNAPSHOT built at Tue, 4 Jan 2022 16:50:23 -0800.
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