strelka

SNP and indel caller from mapped paired-end sequencing reads. This tool is not accelerated, and the original precompiled binary will be run on the server.

Quick Start

$ pbrun strelka \
    --ref Ref/Homo_sapiens_assembly38.fasta \
    --in-tumor-bam tumor.bam \
    --in-normal-bam normal.bam \
    --indel-candidates candidates.vcf \
    --out-prefix output

strelka Reference

Analyze germline variation in small cohorts and somatic variation in tumor/normal sample pairs.

Input/Output file options

--ref REF

Path to the reference file. (default: None)

Option is required.

--in-tumor-bam IN_TUMOR_BAM

(Somatic mode only) Path of BAM/CRAM file for tumor reads. This argument is required to run in somatic mode. (default: None)

--in-normal-bam IN_NORMAL_BAM

(Somatic mode only) Path of BAM/CRAM file for normal reads. This argument is required to run in somatic mode. (default: None)

--in-bams IN_BAMS

(Germline mode only) Path of BAM/CRAM file for reads. This argument is required to run in germline mode and can be specified multiple times. The path can be a (default: None)

--indel-candidates INDEL_CANDIDATES

Path to a VCF of candidate indel alleles. Must be in vcf/vcf.gz format. This option can be used multiple times. (default: None)

--bed BED

Optional bgzip-compressed/tabix-indexed BED file containing the set of regions to call. (default: None)

--out-prefix OUT_PREFIX

Prefix filename for output data. (default: None)

Option is required.

Options specific to this tool

--num-threads NUM_THREADS

Number of threads for worker. (default: 12)

--strelka-options STRELKA_OPTIONS

Pass supported strelka options as one string. e.g. --strelka-options="--exome". (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.