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.