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Germline WGS

DRAGEN Recipe - Germline WGS

Overview

This recipe is for processing whole genome sequencing data for germline 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.

We highly recommend using a pangenome reference for human samples (excluding RNA). For more details, refer to Dragen Reference Support.

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

#!/bin/bash
set -euo pipefail

# Path to DRAGEN hashtable
DRAGEN_HASH_TABLE=<REF_DIR>  # pangenome reference for human samples

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

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

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

INPUT_FASTQ="
  --fastq-file1 $FASTQ1 \
  --fastq-file2 $FASTQ2 \
  --RGSM $RGSM \
  --RGID $RGID \
"

INPUT_BAM="
  --bam-input $BAM \
"

INPUT_CRAM="
  --cram-input $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-enable-self-normalization true \
"

SNV_OPTIONS="
  --enable-variant-caller true \
"

SV_OPTIONS="
  --enable-sv true \
"

TARGETED_OPTIONS="
  --enable-targeted true \
"

PGX_OPTIONS="
  --enable-pgx true \
"

STR_OPTIONS="
  --repeat-genotype-enable true \
"

# Automatic merging of VNTR calls into SV VCF disabled with the second option
# See the VNTR calling page for more details
VNTR_OPTIONS="
  --enable-vntr true \
  --sv-vntr-merge false \
"

HLA_OPTIONS="
--enable-hla=true \
--hla-enable-class-2=true \ 
"

# Construct final command line
CMD="
  dragen \
  $INPUT_OPTIONS \
  $OUTPUT_OPTIONS \
  $MA_OPTIONS \
  $CNV_OPTIONS \
  $SNV_OPTIONS \
  $SV_OPTIONS \
  $TARGETED_OPTIONS \
  $PGX_OPTIONS \
  $STR_OPTIONS \
  $VNTR_OPTIONS \
  $HLA_OPTIONS \
"

# Execute
echo $CMD
bash -c $CMD

Additional Notes and Options

Optional settings per component are listed below. Full option list at this page.

SNV

Note that we do not recommend changing the default QUAL thresholds of 3 for DRAGEN-ML and 10 for DRAGEN without ML. These values differ from each other because DRAGEN-ML improves the calibration of QUAL scores, leading to a change in the scoring range (see QUAL, QD, and GQ Formulation).

HLA