annotatebamwithumis
Annotates existing BAM files with UMIs (Unique Molecular Indices) from a separate FASTQ file.
$ pbrun annotatebamwithumis \
--in-fq input_fastq_with_UMI_reads.fastq \
--in-bam input.bam \
--out-bam output.bam
Annotates existing BAM files with UMIs (Unique Molecular Indices) from a separate FASTQ file.
Input/Output file options
- --in-fq IN_FQ
- --in-bam IN_BAM
- --out-bam OUT_BAM
Path to the input FASTQ file with UMI reads. (default: None)
Option is required.
Path to the input BAM file. (default: None)
Option is required.
Path of output BAM file. (default: None)
Option is required.
Options specific to this tool
(none)
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.