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Somatic_hybridization_panel.sh
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#!/bin/sh
# Copyright (c) 2016-2024 Sentieon Inc. All rights reserved
# *******************************************
# Script to perform TNscope variant calling on
# hybridization captured tumor sample with
# coverage over 200x and a matched normal sample.
# *******************************************
set -eu
# Update with the fullpath location of your sample fastq
TUMOR_SM="tumor_sample" #sample name
TUMOR_RGID="rg_$TUMOR_SM" #read group ID
NORMAL_SM="normal_sample" #sample name
NORMAL_RGID="rg_$NORMAL_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
NORMAL_FASTQ_1="$FASTQ_FOLDER/normal_1.fastq.gz"
NORMAL_FASTQ_2="$FASTQ_FOLDER/normal_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
# Other settings
NT=$(nproc) #number of threads to use in computation, set to number of cores in the server
START_DIR="$PWD/test/TNscope" #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
# ******************************************
# 1a. Mapping reads with BWA-MEM, sorting for the tumor sample
# ******************************************
#The results of this call are dependent on the number of threads used. To have number of threads independent results, add chunk size option -K 10000000
( $SENTIEON_INSTALL_DIR/bin/sentieon bwa mem -R "@RG\tID:$TUMOR_RGID\tSM:$TUMOR_SM\tPL:$PL" \
-t $NT -K 10000000 $FASTA $TUMOR_FASTQ_1 $TUMOR_FASTQ_2 || \
{ echo -n 'BWA error'; exit 1; } ) | \
$SENTIEON_INSTALL_DIR/bin/sentieon util sort -o tumor_sorted.bam -t $NT --sam2bam -i - || \
{ echo "Alignment1 failed"; exit 1; }
# ******************************************
# 1b. Mapping reads with BWA-MEM, sorting for the normal sample
# ******************************************
#The results of this call are dependent on the number of threads used. To have number of threads independent results, add chunk size option -K 10000000
( $SENTIEON_INSTALL_DIR/bin/sentieon bwa mem -R "@RG\tID:$NORMAL_RGID\tSM:$NORMAL_SM\tPL:$PL" \
-t $NT -K 10000000 $FASTA $NORMAL_FASTQ_1 $NORMAL_FASTQ_2 || \
{ echo -n 'BWA error'; exit 1; } ) | \
$SENTIEON_INSTALL_DIR/bin/sentieon util sort -o normal_sorted.bam -t $NT --sam2bam -i - || \
{ echo "Alignment2 failed"; exit 1; }
# ******************************************
# 2a. Metrics for the tumor sample
# ******************************************
$SENTIEON_INSTALL_DIR/bin/sentieon driver -r $FASTA -t $NT -i tumor_sorted.bam \
--algo MeanQualityByCycle tumor_mq_metrics.txt \
--algo QualDistribution tumor_qd_metrics.txt --algo GCBias \
--summary tumor_gc_summary.txt tumor_gc_metrics.txt --algo AlignmentStat \
--adapter_seq '' tumor_aln_metrics.txt \
--algo InsertSizeMetricAlgo tumor_is_metrics.txt \
--algo CoverageMetrics --omit_base_output tumor_coverage_metrics || \
{ echo "Metrics1 failed"; exit 1; }
$SENTIEON_INSTALL_DIR/bin/sentieon plot GCBias -o tumor_gc-report.pdf tumor_gc_metrics.txt
$SENTIEON_INSTALL_DIR/bin/sentieon plot QualDistribution \
-o tumor_qd-report.pdf tumor_qd_metrics.txt
$SENTIEON_INSTALL_DIR/bin/sentieon plot MeanQualityByCycle \
-o tumor_mq-report.pdf tumor_mq_metrics.txt
$SENTIEON_INSTALL_DIR/bin/sentieon plot InsertSizeMetricAlgo \
-o tumor_is-report.pdf tumor_is_metrics.txt
# ******************************************
# 2b. Metrics for the normal sample
# ******************************************
$SENTIEON_INSTALL_DIR/bin/sentieon driver -r $FASTA -t $NT -i normal_sorted.bam \
--algo MeanQualityByCycle normal_mq_metrics.txt \
--algo QualDistribution normal_qd_metrics.txt --algo GCBias \
--summary normal_gc_summary.txt normal_gc_metrics.txt --algo AlignmentStat \
--adapter_seq '' normal_aln_metrics.txt \
--algo InsertSizeMetricAlgo normal_is_metrics.txt \
--algo CoverageMetrics --omit_base_output normal_coverage_metrics || \
{ echo "Metrics2 failed"; exit 1; }
$SENTIEON_INSTALL_DIR/bin/sentieon plot GCBias -o normal_gc-report.pdf normal_gc_metrics.txt
$SENTIEON_INSTALL_DIR/bin/sentieon plot QualDistribution \
-o normal_qd-report.pdf normal_qd_metrics.txt
$SENTIEON_INSTALL_DIR/bin/sentieon plot MeanQualityByCycle \
-o normal_mq-report.pdf normal_mq_metrics.txt
$SENTIEON_INSTALL_DIR/bin/sentieon plot InsertSizeMetricAlgo \
-o normal_is-report.pdf normal_is_metrics.txt
# ******************************************
# 3a. Remove duplicate reads for the tumor sample.
# 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 \
--fun score_info tumor_score.txt || { echo "LocusCollector1 failed"; exit 1; }
$SENTIEON_INSTALL_DIR/bin/sentieon driver -t $NT -i tumor_sorted.bam --algo Dedup \
--score_info tumor_score.txt --metrics tumor_dedup_metrics.txt tumor_deduped.bam || \
{ echo "Dedup1 failed"; exit 1; }
# ******************************************
# 3b. Remove duplicate reads for the normal sample.
# 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 normal_sorted.bam --algo LocusCollector \
--fun score_info normal_score.txt || { echo "LocusCollector2 failed"; exit 1; }
$SENTIEON_INSTALL_DIR/bin/sentieon driver -t $NT -i normal_sorted.bam --algo Dedup \
--score_info normal_score.txt --metrics normal_dedup_metrics.txt normal_deduped.bam || \
{ echo "Dedup2 failed"; exit 1; }
# ******************************************
# 4. Somatic and Structural variant calling
# ******************************************
# Consider adding `--disable_detector sv` if not interested in SV calling
$SENTIEON_INSTALL_DIR/bin/sentieon driver -r $FASTA -t $NT \
${INTERVAL_FILE:+--interval $INTERVAL_FILE} \
-i tumor_deduped.bam -i normal_deduped.bam \
--algo TNscope \
--tumor_sample $TUMOR_SM --normal_sample $NORMAL_SM \
--dbsnp $KNOWN_DBSNP \
--min_tumor_allele_frac 0.009 \
--max_fisher_pv_active 0.05 \
--max_normal_alt_cnt 10 \
--max_normal_alt_frac 0.01 \
--max_normal_alt_qsum 250 \
--sv_mask_ext 10 \
--prune_factor 0 \
--assemble_mode 2 \
output_tnscope.pre_filter.vcf.gz || \
{ echo "TNscope failed"; exit 1; }
# ******************************************
# 5. Variant filtration
# ******************************************
$SENTIEON_INSTALL_DIR/bin/sentieon pyexec $TNSCOPE_FILTER \
-v output_tnscope.pre_filter.vcf.gz \
--tumor_sample $TUMOR_SM \
-x tissue_panel --min_tumor_af 0.0095 --min_depth 200 \
output_tnscope.filter.vcf.gz || \
{ echo "TNscope filter failed"; exit 1; }