RNA WTS

#!/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 \
"

# You could use the tumor fastq options to provide the FASTQ files.
INPUT_TUMOR_FASTQ="
  --tumor-fastq1 $FASTQ1 \
  --tumor-fastq2 $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 \
"

# RNA aligner requires an annotation file in GTF or GFF3 format.
GTF=<GTF_PATH>

# RNA pipeline requires map-align to be true.
RNA_MAP_OPTIONS="
  --enable-rna true \
  --enable-map-align true \
  --annotation-file $GTF \
"

# You should set the library according to the read orientations.
# The options are IU, ISR, ISF, U, SR, or SF. Or set it to A to automatically detect the correct read orientation.
QUANT_OPTIONS="
  --enable-rna-quantification true \
  --rna-library-type IU \
  --rna-quantification-gc-bias true \
"

SPLICE_OPTIONS="
  --enable-rna-splice-variant true \
"

FUSION_OPTIONS="
  --enable-rna-gene-fusion true \
"

# To call variants, you need to set a bed file with target regions to call. 
# This bed could contain all exones.
VARIANT_OPTIONS="
  --enable-variant-caller true \
  --vc-target-bed $TARGET_BED
"

# Construct final command line
CMD="
  dragen \
  $INPUT_OPTIONS \
  $OUTPUT_OPTIONS \
  $RNA_MAP_OPTIONS \
  $QUANT_OPTIONS \
  $SPLICE_OPTIONS \
  $FUSION_OPTIONS \
  $VARIANT_OPTIONS 
"

# Execute
echo $CMD
bash -c $CMD