Somatic_ctDNA_with_UMI.sh

#!/bin/sh

# Copyright (c) 2016-2024 Sentieon Inc. All rights reserved

# *******************************************
# Script to perform TNscope variant calling on
# UMI-tagged samples
# *******************************************

set -eu

# Update with the fullpath location of your sample fastq
TUMOR_SM="tumor_sample" #sample name
TUMOR_RGID="rg_$TUMOR_SM" #read group ID
PL="ILLUMINA" #or other sequencing platform
FASTQ_FOLDER="/home/pipeline/samples"
TUMOR_FASTQ_1="$FASTQ_FOLDER/tumor_1.fastq.gz"
TUMOR_FASTQ_2="$FASTQ_FOLDER/tumor_2.fastq.gz" #If using Illumina paired data

# Update with the location of the reference data files
FASTA_DIR="/home/regression/references/b37"
FASTA="$FASTA_DIR/human_g1k_v37_decoy.fasta"
KNOWN_DBSNP="$FASTA_DIR/dbsnp_138.b37.vcf.gz"
INTERVAL_FILE="targeted_regions.bed"

# Update with the location of the Sentieon software package and license file
SENTIEON_INSTALL_DIR=/home/release/sentieon-genomics-|release_version|
TNSCOPE_FILTER=/home/sentieon-scripts/tnscope_filter/tnscope_filter.py
export SENTIEON_LICENSE=/home/Licenses/Sentieon.lic #or using licsrvr: c1n11.sentieon.com:5443

#UMI information
READ_STRUCTURE="12M11S+T,+T" #an example duplex: "3M2S+T,3M2S+T" where duplex UMI extraction requires an identical read structure for both strands
DUPLEX_UMI="false" #set to "true" if duplex

# Other settings
NT=$(nproc) #number of threads to use in computation, set to number of cores in the server
START_DIR="$PWD/test/TNscope_umi" #Determine where the output files will be stored

# ******************************************
# 0. Setup
# ******************************************
WORKDIR="$START_DIR"
mkdir -p $WORKDIR
LOGFILE=$WORKDIR/run.log
exec >$LOGFILE 2>&1
cd $WORKDIR

# ******************************************
# 1. Pre-processing of FASTQ containing UMIs
# ******************************************
if [ "$DUPLEX_UMI" = "true" ] ; then
    READ_STRUCTURE="-d $READ_STRUCTURE"
fi
( $SENTIEON_INSTALL_DIR/bin/sentieon umi extract $READ_STRUCTURE $TUMOR_FASTQ_1 $TUMOR_FASTQ_2 || \
    { echo -n 'Extract error' >&2; exit -1; } ) | \
  ( $SENTIEON_INSTALL_DIR/bin/sentieon bwa mem -p -C \
  -R "@RG\tID:$TUMOR_RGID\tSM:$TUMOR_SM\tPL:$PL" -t $NT \
  -K 10000000 $FASTA - || { echo -n 'BWA error'; exit 1; } ) | \
  $SENTIEON_INSTALL_DIR/bin/sentieon util sort -t $NT -r $FASTA --sam2bam -i - \
  -o tumor_sorted.bam || \
  { echo "Alignment failed"; exit 1; }

# ******************************************
# 2. Remove duplicate reads for the tumor sample
# use the consensus-based approach with UMI.
# It is possible to remove instead of mark
# duplicates by adding the --rmdup option in Dedup
# ******************************************
$SENTIEON_INSTALL_DIR/bin/sentieon driver -t $NT -i tumor_sorted.bam --algo LocusCollector \
    --consensus --umi_tag XR --fun score_info tumor_score.txt || { echo "LocusCollector failed"; exit 1; }

$SENTIEON_INSTALL_DIR/bin/sentieon driver -t $NT -i tumor_sorted.bam -r $FASTA --algo Dedup \
    --score_info tumor_score.txt --metrics umi.dedup_metrics.txt tumor_deduped.bam || \
    { echo "Dedup failed"; exit 1; }

# ******************************************
# 3. Somatic and Structural variant calling
# ******************************************
$SENTIEON_INSTALL_DIR/bin/sentieon driver -r $FASTA -t $NT -i tumor_deduped.bam \
    ${INTERVAL_FILE:+--interval $INTERVAL_FILE} \
    --algo TNscope \
    --tumor_sample $TUMOR_SM \
    --dbsnp $KNOWN_DBSNP \
    --disable_detector sv \
    --min_tumor_allele_frac 3e-3 \
    --min_tumor_lod 3.0 \
    --min_init_tumor_lod 1.0 \
    --assemble_mode 4 \
    --pcr_indel_model NONE \
    --min_base_qual 40 \
    --resample_depth 100000 \
    output_tnscope.pre_filter.vcf.gz || \
    { echo "TNscope failed"; exit 1; }

# ******************************************
# 4. Variant filtration
# ******************************************
$SENTIEON_INSTALL_DIR/bin/sentieon pyexec $TNSCOPE_FILTER \
    -v output_tnscope.pre_filter.vcf.gz \
    --tumor_sample $TUMOR_SM \
    -x ctdna --min_tumor_af 0.001 --min_depth 1000 \
    output_tnscope.filter.vcf.gz || \
    { echo "TNscope filter failed"; exit 1; }