Outline

ciscall run executes variant calling pipelines including the following modules:

  • cisMuton (SNVs/indels)
  • cisCton (copy number alterations)
  • cisFusion (fusion genes)

Example of command-line execution:

$ ciscall run \
    --analysis-modes MUTON:WGENOME CTON:WGENOME FUSION:WGENOME \
    --fg-r1-fastq /path/to/test_tumor.fastq.R1.gz \
    --fg-r2-fastq /path/to/test_tumor.fastq.R2.gz \
    --bg-r1-fastq /path/to/test_normal.fastq.R1.gz \
    --bg-r2-fastq /path/to/test_normal.fastq.R2.gz \
    --target-enrich SureSelect \
    --specimen FFPE \
    --target-bed /path/to/TESTPANEL.target.bed \
    --fusion-bed /path/to/TESTPANEL.fusion.bed \
    --genome-fa /path/to/ucsc_human_b37_chr1-22-X-Y-M.fa \
    --refgene-txt /path/to/refGene.txt \
    --snp-vcf /path/to/test_snp.vcf.gz \
    --mapability-bigwig /path/to/wgEncodeDukeMapabilityUniqueness20bp.bigWig \
    --gene-bed /path/to/hg19.gene.bed \
    --fusion-gene-txt /path/to/main_fusion_gene.txt \
    --gene-family-txt /path/to/genefamilies.txt \
    --decoy-fa /path/to/hs37d5cs.fa

Options

Option flag Required Description
--target-bed BED_FILE Yes Path to a target region bed file
--fusion-bed FUSION_FILE Yes Path to a fusion region bed file
--genome-fa GENOME_FA_FILE Yes Path to a reference genome file
--refgene-txt REFGENE_FILE Yes Path to a RefGene file
--snp-vcf SNPS_FILE Yes (MUTON) Path to a snp vcf file
--mapability-bigwig MAPABILITY_FILE Yes (CTON) Path to a mapability bigWig file
--gene-bed GENE_REGION_FILE Yes (FUSION) Path to a gene region bed file
--fusion-gene-txt FUSION_GENE_FILE Yes (FUSION) Path to a fusion gene pair file
--gene-family-txt GENE_FAMILY_FILE Yes (FUSION) Path to a gene family tsv file
--decoy-fa DECOY_FILE No Path to a mapping decoy FASTA file
--fg-r1-fastq FG_FASTQ_R1_FILE Yes Path to a foreground FASTQ read1 file
--fg-r2-fastq FG_FASTQ_R2_FILE Yes Path to a foreground FASTQ read2 file
--bg-r1-fastq BG_FASTQ_R1_FILE Yes Path to a background FASTQ read1 file
--bg-r2-fastq BG_FASTQ_R2_FILE Yes Path to a background FASTQ read2 file
--fg-sam No Path to a foreground BAM/CARM file
--bg-sam No Path to a background BAM/CRAM file
--work-dir WORK_DIR No Path to a working directory
--custom-ref-dir CUSTOM_REF_DIR No Path to a custom reference directory
--analysis-modes MODULE:MAPPING ... No Analysis modes
--target-enrich CAPTURE_METHOD No Target capture method
--specimen SPECIMEN No Specimen type
--skip-dedup No Skip duplicate removal
--random-seed RANDOM_SEED No Random seed
--threads THREAD_NUM No Number of thread
--max-memory-gb MAX_MEMORY No Max memory GB unit
--cutadapt CUTADAPT No Path to cutadapt
--pigz PIGZ No Path to pigz
--bwa BWA No Path to bwa
--samtools SAMTOOLS No Path to samtools
--bigWigToBedGraph BIGWIGTOBEDGRAPH No Path to bigWigToBedGraph
--console-log-lv CONSOLE_LOG_LV No Console log level
--cna-baseline-bed CNA_BASELINE_FILE No Path to a CNA baseline file
--adapter-txt ADAPTER_FILE No Path to an adapter file
--bwa-mode BWA_MODE No BWA mapping mode
--ignore-error IGNORE_ERROR No Ignore errors in child processes
--only-mapping No Execute read mapping and exit
--no-mapping No Skip read mapping
--custom-param-yml CUSTOM_PARAM_FILE No Path to a parameter YAML file
--igv-sh IGV_SH No Path to igv.sh in IGV

--target-bed: Target Panel BED File

  • BED file of target-capture regions.
    • Tab-delimited file without a header in ascending order by start position.
    • Columns: Chromosome number, start position (1-based), end position (1-based)

--fusion-bed: Fusion Bed File

  • BED file for regions including possible breakpoints of fusion genes.
    • Tab-delimited file without a header in ascending order by start position.
    • Columns: Chromosome number, start position (1-based), end position (1-based), gene name

--genome-fa: Reference Genome File

  • FASTA file of reference genome.
    • Concatenate into a single FASTA in ascending order by start position.

--refgene-txt: Refgene File

--snp-vcf: SNP File

  • Gzipped VCF file for SNP.
  • Used by cisMuton.
  • The values for QUAL, FILTER, and INFO columns are ignored.

--mapability-bigwig: Mapability File

--gene-family-txt: Gene Family File

--gene-bed: Gene Region BED File

  • BED file of all gene regions.
  • Used by cisFusion.

--fusion-gene-txt: Fusion Gene File

  • Text file for fusion gene pairs.
  • Used by cisFusion.

--decoy-fa: Decoy Sequence FASTA File

--fg-r1-fastq, --fg-r2-fastq, --bg-r1-fastq, --bg-r2-fastq: FASTQ Files of Samples

  • Gzipped FASTQ files of foreground and background (control) samples.
    • --fg-r1-fastq: Path to a read1 FASTQ of a foregroud sample
    • --fg-r2-fastq: Path to a read2 FASTQ of a foregroud sample
    • --bg-r1-fastq: Path to a read1 FASTQ of a backgroud sample
    • --bg-r2-fastq: Path to a read2 FASTQ of a backgroud sample
  • Paired-end reads use all the options.
    • The following file extensions are recommended for paired-end reads:
      • <sample>.R1.fastq.gz, <sample>.R2.fastq.gz
      • <sample>.fastq.R1.gz, <sample>.fastq.R2.gz
    • cisFusion uses only --fg-r1-fastq, --fg-r2-fastq.
  • Single-end reads use only --fg-r1-fastq and --bg-r1-fastq.
    • cisFusion uses only --fg-r1-fastq.

--fg-sam, --bg-sam: BAM/CRAM Files of Samples

  • BAM files of foreground and background samples.
  • cisFusion can work without --bg-sam if you don’t need germline SV.

--work-dir: Working Directory

  • Working directory of ciscall run.
  • Output files of cisCall are created in this.
  • Default: .

--custom-ref-dir: Custom Reference Directory

  • Reference directory of ciscall run.
  • cisCall creates reference files in this.
    • By default, a reference directory is created in a working directory.

--analysis-modes: Analysis Modes

  • Sets of cisCall’s variant calling modules and their mapping mode (mapping region)
    • Choices:
      • MUTON:WGENOME (cisMuton)
      • CTON:WGENOME (cisCton)
      • FUSION:WGENOME (cisFusion)
    • cisCall run modules passed by this option.
      • If MUTON:WGENOME is given, cisCall run only cisMuton.
      • If MUTON:WGENOME CTON:WGENOME is given, cisCall run cisMuton and cisCton.
  • Default: MUTON:WGENOME CTON:WGENOME FUSION:WGENOME

--target-enrich: Target Enrich Method

  • Target enrichment method.
  • Choices:
    • SureSelect (default)
    • HaloPlex
    • TargetSeq (under development)
    • AmpliSeq (under development)

--specimen: Specimen Type

  • A specimen type of the target (foreground) sample.
  • Choices:
    • FFPE (default)
    • Frozen

--skip-dedup: Skip Duplicate Removal

  • Skip duplicate removal with Samtools.

--random-seed: Random Seed

  • Random seed.

--threads: Maximum threads

  • Maximum number of threads/processes for cisCall.
  • Deafault: Number of CPU cores in a system.

--max-memory-gb: Maximum Memory

  • Maximum size (GB) of memory for cisCall.
  • Default: Total amount of memory in a system

--cutadapt: Cutadapt

  • Path to cutadapt command (including command name).
  • Default: Path from the PATH environment variable.

--pigz: Pigz

  • Path to pigz command (including command name).
  • Default: Path from the PATH environment variable.

--bwa: BWA

  • Path to bwa command (including command name).
  • Default: Path from the PATH environment variable.

--samtools: Samtools

  • Path to samtools command (including command name).
  • Default: Path from the PATH environment variable.

--bigWigToBedGraph: bigWigToBedGraph

  • Path to bigWigToBedGraph command (including command name).
  • Default: Path from the PATH environment variable.

--console-log-lv: Console Log Level

  • Logging level for console.
  • Choices: WARNING(default) / DEBUG / INFO

--cna-baseline-bed: CNA Baseline File

  • BED file of CNA baseline regions.
    • Tab-delimited file without a header in ascending order by start position.
    • Columns: Chromosome number, start position (1-based), end position (1-based)
  • Regions are interpreted as CNA baseline regions for cisCton to define amplifications or losses.
  • Regions should be included in the target panel bed file.

--adapter-txt: Adapter File

  • This option is deprecated.
  • Path to an adapter file.
  • Adapter removal is executed if this is given.

--bwa-mode: BWA mode

  • This option is deprecated.
  • BWA algorithm for mapping.

--ignore-error: Ignore Errors in Child processes

  • Developer option.
  • Ignore errors in child processes.

--only-mapping: Execute Read Mapping and Exit

  • Developer option.
  • Execute read mapping and exit without variant calling.

--no-mapping: Skip Read Mapping

  • Developer option.
  • Skip read mapping.

--custom-param-yml: Parameter YAML File

  • Developer option.
  • Path to a customized parameter YAML file.

--igv-sh: IGV Shell Fle

  • Developer option.
  • Path to igv.sh in IGV.

Output

ciscall run creates the following directories:

  • output/: result files
  • ref/: reference files
  • tmp/: temporary working files

cisCall output results files with VCF format in output/.

See the following pages for more details: