Convert FASTQs to an unaligned BAM file.
Run fq2ubam to convert FASTQs to an unaligned BAM file.
Input/Output file options
- --in-fq IN_FQ
- --ref REF
- --out-bam OUT_BAM
IN_FQ Path to pair ended FASTQ files. Files can be in fastq or fastq.gz format. (default: None)
Option is required.
Path to the reference file. Required if --sort-order is not unsorted. (default: None)
Path to the output BAM file. (default: None)
Option is required.
Options specific to this tool
- --sample-name SAMPLE_NAME
- --num-threads NUM_THREADS
- --comment COMMENT
- --description DESCRIPTION
- --library-name LIBRARY_NAME
- --platform PLATFORM
- --platform-model PLATFORM_MODEL
- --platform-unit PLATFORM_UNIT
- --predicted-insert-size PREDICTED_INSERT_SIZE
- --program-group PROGRAM_GROUP
- --read-group-name READ_GROUP_NAME
- --run-date RUN_DATE
- --sequencing-center SEQUENCING_CENTER
- --sort-order SORT_ORDER
- --quality-format QUALITY_FORMAT
- --min-q MIN_Q
- --max-q MAX_Q
- --num-zip-threads NUM_ZIP_THREADS
- --num-sort-threads NUM_SORT_THREADS
- --max-records-in-ram MAX_RECORDS_IN_RAM
Sample name to insert into the read group header. (default: None)
Option is required.
Number of worker threads. (default: 6)
Comment(s) to include in the merged output file's header. Option can be used more than once. (default: None)
Inserted into the read group header. (default: None)
The library name to place into the LB attribute in the read group header. (default: None)
The platform type (e.g. illumina, solid) to insert into the read group header. (default: None)
Platform model to insert into the group header (free-form text providing further details of the platform/technology used). (default: None)
The platform unit (often run_barcode.lane) to insert into the read group header. (default: None)
Predicted median insert size, to insert into the read group header. (default: None)
Program group to insert into the read group header. (default: None)
Read group name to insert into the read group header and added as an attribute to each output read. (default: A)
Date the run was produced, to insert into the read group header. Must be in ISO 8601 format (YYYY-MM-DD). (default: None)
The sequencing center from which the data originated. (default: None)
The sort order for the output BAM file. Possible values are {unsorted,queryname,coordinate}. (default: queryname)
A value describing how the quality values are encoded in the input FASTQ file. Possible values are either Solexa (phred scaling + 66), Illumina (phred scaling + 64), or Standard (phred scaling + 33). (default: Standard)
Minimum quality allowed in the input fastq. Value must be >= 0. (default: 0)
Maximum quality allowed in the input fastq. Value must be <= 93. (default: 93)
Number of CPUs to use for zipping bam files in a run (default 16 for coordinate sorts and 10 otherwise) (default: None)
Number of CPUs to use for sorting in a run (default 10 for coordinate sorts and 16 otherwise) (default: None)
Maximum number of records in RAM when using a queryname or template coordinate sort mode; lowering this number will decrease maximum memory usage. (default: 65000000)
Common options:
- --logfile LOGFILE
- --tmp-dir TMP_DIR
- --with-petagene-dir WITH_PETAGENE_DIR
- --keep-tmp
- --license-file LICENSE_FILE
- --no-seccomp-override
- --version
Path to the log file. If not specified, messages will only be written to the standard error output. (default: None)
Full path to the directory where temporary files will be stored.
Full path to the PetaGene installation directory. By default, this should have been installed at /opt/petagene. Use of this option also requires that the PetaLink library has been preloaded by setting the LD_PRELOAD environment variable. Optionally set the PETASUITE_REFPATH and PGCLOUD_CREDPATH environment variables that are used for data and credentials (default: None)
Do not delete the directory storing temporary files after completion.
Path to license file license.bin if not in the installation directory.
Do not override seccomp options for docker (default: None).
View compatible software versions.
The --in-fq option takes the names of two FASTQ files, optionally followed by a quoted read group. The FASTQ filenames must not start with a hyphen.