Somatic WGS Tumor Only

This recipe is for processing whole genome sequencing data for somatic tumor only workflows.

Example Command Line

For most scenarios, simply creating the union of the command line options from the single caller scenarios will work.

•

Configure the INPUT options

•

Configure the OUTPUT options

•

Configure MAP/ALIGN depending on if realignment is desired or not

•

Configure the VARIANT CALLERs based on the application

•

Configure any additional options

•

Build up the necessary options for each component separately, so that they can be re-used in the final command line.

The following are partial templates that can be used as starting points. Adjust them accordingly for your specific use case:

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#!/bin/bash
set -euo pipefail

# Path to DRAGEN hashtable
DRAGEN_HASH_TABLE=<REF_DIR>

# Path to output directory for the DRAGEN run
OUTPUT=<OUT_DIR>

# File prefix for DRAGEN output files
PREFIX=<OUT_PREFIX>

# Population SNP VCF. It can be retrieved from catalogs of population variation
# such as the 1000 genome project or other large cohort discovery efforts.
# Only high-frequency SNPs should be included. A suitable file can be retrieved
# from the GATK resource bundle: 1000G_phase1.snps.high_confidence.vcf.gz
CNV_POP_VCF=<POPULATION_VCF_PATH>

# Path to VC systematic noise BED file. In tumor-only variant calling, this filter
# is essential for removing systematic noise observed in normal samples. Prebuilt
# systematic noise files are available for download on the Illumina DRAGEN Bio-IT 
# Platform support site page. Alternatively, running the somatic TO pipeline on
# normal samples can generate a systematic noise file. We recommend using a
# systematic noise file based on normal samples that match the library prep of
# the tumor samples. A prebuilt systematic noise BED file can be downloaded from
# https://support.illumina.com/sequencing/sequencing_software/dragen-bio-it-platform/product_files.html
VC_SYSTEMATIC_NOISE_FILE=<VC_SYSTEMATIC_NOISE_BED_FILE_PATH>

# The Nirvana annotation database is downloadable at 
# https://support-docs.illumina.com/SW/DRAGEN_v310/Content/SW/DRAGEN/IAE_DownloadData.htm
NIRVANA_ANNOTATION_FOLDER=<NIRVANA_ANNOTATION_FOLDER_PATH>

# Define the input sources, select fastq list, fastq, bam, or cram.
INPUT_FASTQ_LIST="
  --tumor-fastq-list $TUMOR_FASTQ_LIST \
  --tumor-fastq-list-sample-id $TUMOR_FASTQ_LIST_SAMPLE_ID \
"

INPUT_FASTQ="
  --tumor-fastq1 $TUMOR_FASTQ1 \
  --tumor-fastq2 $TUMOR_FASTQ2 \
  --RGSM-tumor $RGSM_TUMOR \
  --RGID-tumor $RGID_TUMOR \
"

INPUT_BAM="
  --tumor-bam-input $TUMOR_BAM \
"

INPUT_CRAM="
  --tumor-cram-input $TUMOR_CRAM \
"

# Select input source, here in this example we use INPUT_FASTQ_LIST
INPUT_OPTIONS="
  --ref-dir $DRAGEN_HASH_TABLE \
  $INPUT_FASTQ_LIST \
"

OUTPUT_OPTIONS="
  --output-directory $OUTPUT \
  --output-file-prefix $PREFIX \
"

MA_OPTIONS="
  --enable-map-align true \
  --enable-sort true \
  --enable-duplicate-marking true \
"

CNV_OPTIONS="
  --enable-cnv true \
  --cnv-population-b-allele-vcf $CNV_POP_VCF \
"

SNV_OPTIONS="
  --enable-variant-caller true \
  --vc-systematic-noise $VC_SYSTEMATIC_NOISE_FILE \
  --vc-enable-germline-tagging true \
  --enable-variant-annotation true \
  --variant-annotation-data $NIRVANA_ANNOTATION_FOLDER \
  --variant-annotation-assembly $REFERENCE \
"

SV_OPTIONS="
  --enable-sv true \
  --sv-systematic-noise $SV_SYSTEMATIC_NOISE_BEDPE \
"

SNV_SV_DEDUPLICATION_OPTIONS="
  --enable-variant-deduplication true \
"

# Construct final command line
CMD="
  dragen \
  $INPUT_OPTIONS \
  $OUTPUT_OPTIONS \
  $MA_OPTIONS \
  $CNV_OPTIONS \
  $SNV_OPTIONS \
  $SV_OPTIONS \
  $SNV_SV_DEDUPLICATION_OPTIONS \
"

# Execute
echo $CMD
bash -c $CMD