annotatebamwithumis¶
Annotates existing BAM files with UMIs (Unique Molecular Indices) from a separate FASTQ file.
Quick Start¶
$ pbrun annotatebamwithumis \
--in-fq input_fastq_with_UMI_reads.fastq \
--in-bam input.bam \
--out-bam output.bam
annotatebamwithumis Reference¶
Annotates existing BAM files with UMIs (Unique Molecular Indices) from aseparate FASTQ file.
Input/Output file options¶
- --in-fq IN_FQ
Path to the input FASTQ file with UMI reads. (default: None)
Option is required.
- --in-bam IN_BAM
Path to the input BAM file. (default: None)
Option is required.
- --out-bam OUT_BAM
Path of output BAM file. (default: None)
Option is required.
Options specific to this tool¶
(none)
Common options:¶
- --logfile LOGFILE
Path to the log file. If not specified, messages will only be written to the standard error output. (default: None)
- --tmp-dir TMP_DIR
Full path to the directory where temporary files will be stored.
- --with-petagene-dir WITH_PETAGENE_DIR
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)
- --keep-tmp
Do not delete the directory storing temporary files after completion.
- --license-file LICENSE_FILE
Path to license file license.bin if not in the installation directory.
- --no-seccomp-override
Do not override seccomp options for docker (default: None).
- --version
View compatible software versions.