ITCC VCF2MAF

Converts the output of the Oncoanalyser pipeline into file formats ready for the ITCC cBioPortal instance

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Requirements

Provided in container form, so the ability to run Docker, Singularity or Apptainer is required.

Minimum System Requirements

• CPUs: 16
• Memory: 32 GB RAM
• Disk: 100 GB+ free space
• Singularity or Docker or Apptainer

Tested on a high performance cluster using slurm scheduler, with these requirements and Singularity version 3.11.3. Compute node requires internet access to download the reference data on first use.

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Usage

The container can be pulled from Dockerhub.

singularity pull itcc_vcf2maf_1_0_0.sif docker://shlienteam/itcc_vcf2maf:1.0.0
singularity exec \
-B /path/to/mount/whole/filesystem \
-B /your/path/to/reference/dir:/resources \
/path/to/your/singularity/image/cache/itcc_vcf2maf_1_0_0.sif \
python /opt/itcc_vcf2maf/pedcan_vcf2maf.py -h

usage: pedcan_vcf2maf.py [-h] [-d DATA_DIR] -r RELEASE_ID -p PAT_SAM [-t TEMP_SPACE] [--dry-run]

ITCC VCF to MAF converter.

options:
  -h, --help            show this help message and exit
  -d DATA_DIR, --dir DATA_DIR
                        The directory to search for vcf and tsv files.
  -r RELEASE_ID, --release_id RELEASE_ID
                        The release id to annotate cbioportal output with.
  -p PAT_SAM, --pat_sam PAT_SAM
                        A TSV file with two columns, patient_id and sample_id.
  -t TEMP_SPACE, --temp TEMP_SPACE
                        The temp space to use.

Singularity options

Given here as /your/path/to/reference/dir, this will be used to store the reference files and vep database required by the pipeline for the first run, and future runs if given a non-temporary directory.

Contents of your reference directory will look like this:
 .
 |-genome
 |---GRCh38_masked_exclusions_alts_hlas.dict
 |---GRCh38_masked_exclusions_alts_hlas.fasta
 |---GRCh38_masked_exclusions_alts_hlas.fasta.fai
 |-vep
 |---af-only-gnomad.hg38.vcf.gz
 |---af-only-gnomad.hg38.vcf.gz.tbi
 |---homo_sapiens
 |-----104_GRCh38

If you don't have access to the internet from the container, you can download and format the resource directory by downloading these files:

genome directory
https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh38_hmf/25.1/GRCh38_masked_exclusions_alts_hlas.fasta

vep directory
https://storage.googleapis.com/gcp-public-data--broad-references/hg38/v0/somatic-hg38/af-only-gnomad.hg38.vcf.gz
https://storage.googleapis.com/gcp-public-data--broad-references/hg38/v0/somatic-hg38/af-only-gnomad.hg38.vcf.gz.tbi
https://ftp.ensembl.org/pub/release-104/variation/vep/homo_sapiens_vep_104_GRCh38.tar.gz

tar -xvf homo_sapiens_vep_104_GRCh38.tar.gz

pedcan_vcf2maf.py options

1. The -t option allows a user specified temporary directory to be given to allow clean up
2. The -d option provides the directory that you wanted scanned and process for files matching .purple.cnv.somatic.tsv or .sage.somatic.vcf.gz.
3. The -r option requests a user specified release id for running the pipeline.
4. The -p option is for the user to provide a TSV file that contains two columns of data with a header line.

Example patient sample tsv file to give with the -p flag.

patient_id	sample_id
patient 1	sample 1
patient 2	sample 2

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Example Command

singularity exec -e -B /your/path/to/reference/dir:/resources \
/path/to/your/singularity/image/cache/itcc_vcf2maf_1_0_0.sif \
python /opt/itcc_vcf2maf/pedcan_vcf2maf.py \
-d /your/path/to/data/dir \
-p /your/path/to/pat_sam.tsv \
-r testing_OA

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Contact

Contact:
- Scott Davidson <scott.davidson@sickkids.ca>