splitncigar

Accelerated SplitNCigarReads functionality from GATK. This tool splits reads that contain Ns in their cigar string (e.g. spanning splicing events in RNAseq data).

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$ pbrun splitncigar \ --ref Ref.fa \ --in-bam in.bam \ --out-bam out.bam

The commands below are the GATK counterpart of the Parabricks command above. The output from these commands will be identical to the output from the above command.

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gatk SplitNCigarReads --reference Ref.fa --input in.bam --output tmp.bam gatk SortSam --java-options -Xmx30g --MAX_RECORDS_IN_RAM=5000000 -I=tmp.bam \ -O=out.bam --SORT_ORDER=coordinate --TMP_DIR=/raid/myrun

Split reads in a BAM file that contain Ns in their cigar string.

Input/Output file options

--ref REF

Path to the reference file. (default: None)

Option is required.

--in-bam IN_BAM

Path to the BAM file. (default: None)

Option is required.

--knownSites KNOWNSITES

Path to a known indels file. The file must be in vcf.gz format. This option can be used multiple times. (default: None)

--out-bam OUT_BAM

Output BAM file. (default: None)

Option is required.

--out-recal-file OUT_RECAL_FILE

Path of the report file after Base Quality Score Recalibration. (default: None)

Tool Options:

--num-cpu-threads NUM_CPU_THREADS

Number of CPU threads to traverse separate chromosomes in splitncigar. (default: 6)

--no-ignore-mark

Do not ignore marked reads in sorted output. (default: 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.

GPU options:

--num-gpus NUM_GPUS

Number of GPUs to use for a run. GPUs 0..(NUM_GPUS-1) will be used.

--gpu-devices GPU_DEVICES

GPU devices to use for a run. By default, all GPU devices will be used. To use specific GPU devices, enter a comma-separated list of GPU device numbers. Possible device numbers can be found by examining the output of the nvidia-smi command. For example, using --gpu-devices 0,1 would only use the first two GPUs.

© Copyright 2023, Nvidia. Last updated on Jun 28, 2023.