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 MUTON:WGENOME CTON:WGENOME FUSION:TARGET \
    --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 \
    --reference-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
--reference-fa REFERENCE_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-bam No Path to a foreground bam file
--bg-bam No Path to a background bam file
--work-dir WORK_DIR No Path to a working directory
--analysis MODULE:MAPPING ... No Analysis module and mapping mode
--target-enrich CAPTURE_METHOD No Target capture method
--specimen SPECIMEN No Specimen type
--skip-duplicate-removal No Skip duplicate removal
--random-seed RANDOM_SEED No random seed
--threads THREAD_NUM No Number of thread
--max-memory MAX_MEMORY No Max memory GB unit
--split No Split bed on CTON segmentation
--name-style NAMES_TYLE No output filename style
--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
--fop FOP No Path to fop
--log LOG_LEVEL No Log level
--adapter-txt ADAPTER_FILE No Path to an adapter file
--fop-xconf No Path to a FOP config file
--param-yml PARAM_FILE No Path to a parameter yaml file

--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), gene name
  • Gene names in the gene name column must be included in refGene.txt.
  • cisCton defines amplifications or deletions using predefined “baseline regions.” Entries (lines) that start with chr in the gene name column are interpreted as baseline regions.

--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

--reference-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-bam, --bg-bam: BAM Files of Samples

  • These options are under development.
  • BAM files of foreground and background samples.
  • cisFusion uses only --fg-bam.

--work-dir: Working Directory

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

--analysis: Analysis Option

  • Sets of cisCall’s variant calling modules and their mapping mode (mapping region)
    • Concatenate one of the variant calling modules and one of the mapping regions like MUTON:WGENOME.
    • Choices:

      Module Selectable Mapping Mode
      MUTON (cisMuton) WGENOME (whole genome) / TARGET (target region)
      CTON (cisCton) WGENOME / TARGET
      FUSION (cisFusion) TARGET / WEXOME (gene region) / WGENOME
    • cisCall run modules passed by this option.
      • If MUTON:WGENOME is given, cisCall run only MUTON.
      • If MUTON:WGENOME CTON:WGENOME is given, cisCall run only MUTON and CTON.
  • Target variant type of the modules:
    • MUTON: SNVs and short indels
    • CTON: copy number alterations
    • FUSION: fusion genes
  • Default: MUTON:WGENOME CTON:WGENOME FUSION:TARGET

--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-duplicate-removal: Skip Duplicate Removal

  • Skip duplicate removal.

--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: Maximum Memory

  • Maximum size (GB) of memory for cisCall.
  • Default: 16

--split: Split Bed on cisCton Segmentation

  • This option is deprecated.
  • Split bed to exon and intron on cisCton segmentation.

--name-style: Output Filename Style

  • This option is deprecated.
  • Output filename style.

--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.

--log: Log Level

  • Log level output in console.
  • Choices: warning(default) / debug / info cisCall run command will create the following directories:

--adapter-txt: Adapter File

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

--fop-xconf: FOP Config File

  • This option is under development.
  • Path to a FOP config file.

--param-yml: Parameter YAML File

  • This option is under development.
  • Path to a customized parameter yaml file.

Output

ciscall run creates the following directories:

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

cisCall output results files with VCF format under output/.

See the following pages for more details: