Germline WGS

#!/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>

# 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