Quick-start dataset

An quick-start dataset (ciscall-quick-start-dataset.tar.gz) is prepared here. This contains the following files:

See cisCall Run Command for more details.

Quick-start tutorial using Docker

This tutorial is triable on Linux or macOS.

  1. Get the source code of cisCall7 (See Request for Download).

  2. Install Docker and Docker Compose.

  3. Make a working directory for quick-start.

    $ mkdir sandbox
    $ cd sandbox
    
  4. Download the quick-start dataset.

    $ wget https://static.ciscall.org/dataset/ciscall-quick-start-dataset.tar.gz
    $ tar xvf ciscall-quick-start-dataset.tar.gz
    $ mv ciscall-quick-start-dataset input
    
  5. Set the environment variables for build and run (optional).

    # User ID and Group ID
    $ export UID="$(id -u)" GID="$(id -g)"
    
    # HTTP proxy (if it exists)
    $ export http_proxy='http://example.proxy.com:8080/'
    $ export https_proxy='https://example.proxy.com:8080/'
    

    UID and GID are used for ownership of output files from a container, and http_proxy and https_proxy are used for image build under proxy.

  6. Build an image of cisCall.

    $ tar xvf /path/to/cisCall7.tar.gz
    $ docker-compose -f cisCall7/docker-compose.yml build
    
  7. Create docker-compose.yml in the current directory (Copy the following YAML snippet).

    docker-compose.yml:

    version: '3'
    
    services:
      ciscall:
        container_name: ciscall
        image: ciscall:latest
        user: ${UID}:${GID}
        volumes:
          - .:/sandbox
        working_dir: /sandbox
        command:
          - run
          - --analysis
          - MUTON:WGENOME
          - CTON:WGENOME
          - FUSION:TARGET
          - --work-dir=./
          - --fg-r1-fastq=./input/test_tumor.fastq.R1.gz
          - --fg-r2-fastq=./input/test_tumor.fastq.R2.gz
          - --bg-r1-fastq=./input/test_normal.fastq.R1.gz
          - --bg-r2-fastq=./input/test_normal.fastq.R2.gz
          - --target-bed=./input/TESTPANEL.target.bed
          - --fusion-bed=./input/TESTPANEL.fusion.bed
          - --reference-fa=./input/ucsc_human_b37_chr1-22-X-Y-M.fa
          - --refgene-txt=./input/refGene.txt
          - --snp-vcf=./input/test_snp.vcf.gz
          - --mapability-bigwig=./input/wgEncodeDukeMapabilityUniqueness20bp.bigWig
          - --gene-bed=./input/hg19.gene.bed
          - --fusion-gene-txt=./input/main_fusion_gene.txt
          - --gene-family-txt=./input/genefamilies.txt
          - --decoy-fa=./input/hs37d5cs.fa
          - --random-seed=0
    

    The command written in the above file is equivalent to the following command:

    $ ciscall run \
        --analysis MUTON:WGENOME CTON:WGENOME FUSION:TARGET \
        --work-dir ./ \
        --fg-r1-fastq ./input/test_tumor.fastq.R1.gz \
        --fg-r2-fastq ./input/test_tumor.fastq.R2.gz \
        --bg-r1-fastq ./input/test_normal.fastq.R1.gz \
        --bg-r2-fastq ./input/test_normal.fastq.R2.gz \
        --target-bed ./input/TESTPANEL.target.bed \
        --fusion-bed ./input/TESTPANEL.fusion.bed \
        --reference-fa ./input/ucsc_human_b37_chr1-22-X-Y-M.fa \
        --refgene-txt ./input/refGene.txt \
        --snp-vcf ./input/test_snp.vcf.gz \
        --mapability-bigwig ./input/wgEncodeDukeMapabilityUniqueness20bp.bigWig \
        --gene-bed ./input/hg19.gene.bed \
        --fusion-gene-txt ./input/main_fusion_gene.txt \
        --gene-family-txt ./input/genefamilies.txt \
        --decoy-fa ./input/hs37d5cs.fa \
        --random-seed 0
    
  8. Check installation.

    $ docker-compose run --rm ciscall --version
    
  9. Download additional asset data.

    $ docker-compose run --rm ciscall download-asset --dest-dir ./input
    $ gzip -d \
        input/ucsc_human_b37_chr1-22-X-Y-M.fa.gz \
        input/refGene.txt.gz \
        input/hs37d5cs.fa.gz
    
  10. Execute variant calling with cisCall.

    $ docker-compose up
    $ docker-compose rm -f        # remove a container
    
  11. Check results of variant calling

    Results are generated in output/ under a working directory (./work in this page.).

    • SNVs/Indels
      • result directory: output/test_tumor.TESTPANEL.target/Muton/
      • vcf file for finally called variant: output/test_tumor.TESTPANEL.target/Muton/Call.test_normal/call.case0_WGENOME_dup.vcf
    • Copy number alterations
      • result directory: output/test_tumor.TESTPANEL.target/Cton/
      • vcf file for finally called variant: output/test_tumor.TESTPANEL.target/Cton/gene.cnv_target_dup.vcf
    • Fusion genes
      • result directory: output/test_tumor.TESTPANEL.target/Fusion/
      • vcf file for finally called variant: output/test_tumor.TESTPANEL.target/Fusion/AlnTarget_LmtBthside_Paired_dup.vcf

See the following pages for more details: