Quick-start dataset

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

fastq files
- Foreground (FFPE sample of tumor tissue)
  - test_tumor.fastq.R1.gz
  - test_tumor.fastq.R2.gz
- Background (Frozen sample of normal tissue)
  - test_normal.fastq.R1.gz
  - test_normal.fastq.R2.gz
asset files
- Target BED
  - TESTPANEL.target.bed
- Fusion BED
  - TESTPANEL.fusion.bed
- Fusion gene pair
  - main_fusion_gene.txt
- Human gene BED
  - hg19.gene.bed
- VCF of SNPs
  - test_snp.vcf.gz

See cisCall Run Command for more details.

Quick-start tutorial using Docker

This tutorial is triable on Linux or macOS.

Get the source code of cisCall7 (See Request for Download).
Install Docker and Docker Compose.
Make a working directory for quick-start.
```
$ mkdir sandbox
$ cd sandbox
```

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

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.

Build an image of cisCall.

$ tar xvf /path/to/cisCall7.tar.gz
$ docker-compose -f cisCall7/docker-compose.yml build

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-mode
      - MUTON:WGENOME
      - CTON:WGENOME
      - FUSION:WGENOME
      - --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
      - --genome-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-mode MUTON:WGENOME CTON:WGENOME FUSION:WGENOME \
    --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 \
    --genome-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

Check installation.

$ docker-compose run --rm ciscall --version

Download additional asset data.

$ docker-compose run --rm ciscall download-asset --dest-dir ./input

Execute variant calling with cisCall.

$ docker-compose up
$ docker-compose rm -f        # remove a container

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/Muton/
  - VCF file for finally called variant:
    - output/test_tumor/Muton/muton_wgenome.vcf
- Copy number alterations
  - result directory: output/test_tumor/Cton/
  - VCF file for finally called variant:
    - output/test_tumor/Cton/gene.cnv_target_dup.vcf
- Fusion genes
  - result directory: output/test_tumor/Fusion/
  - VCF files for finally called variant:
    - output/test_tumor/Fusion/AlnWgenome_LmtOneside_Paired.vcf
    - output/test_tumor/Fusion/AlnWgenome_LmtOneside_Paired_sv.vcf

See the following pages for more details: