ccdg_functional-equivalent.sh

#!/bin/sh

# Copyright (c) 2016-2020 Sentieon Inc. All rights reserved

# *********************************************************************************
# Script to perform DNA seq variant calling using Sentieon following
# the functional equivalent pipeline described in
# https://github.com/CCDG/Pipeline-Standardization/blob/master/PipelineStandard.md
# *********************************************************************************

set -eu

# Update with the fullpath location of your sample FASTQ
SM="sample" #sample name
RGID="rg_$SM" #read group ID
PL="ILLUMINA" #or other sequencing platform
FASTQ_1="${SM}_r1.fastq.gz"
FASTQ_2="${SM}_r2.fastq.gz" #if using 2 FASTQ inputs

# Update with the location of the reference data files
FASTA_DIR="/home/regression/references/hg38bundle"
FASTA="$FASTA_DIR/Homo_sapiens_assembly38.fasta"
KNOWN_DBSNP="$FASTA_DIR/Homo_sapiens_assembly38.dbsnp138.vcf.gz"
KNOWN_INDELS="$FASTA_DIR/Homo_sapiens_assembly38.known_indels.vcf.gz"
KNOWN_MILLS="$FASTA_DIR/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz"

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

# Other settings
NT=$(nproc) #number of threads to use in computation
SAMBLASTER=/home/release/other_tools/samblaster-0.1.23/samblaster
START_DIR="$PWD/test/CCDG" #Determine where the output files will be stored





# You do not need to modify any of the lines below unless you want to tweak the pipeline

# ************************************************************************************************************************************************************************

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

# ******************************************
# 1. Mapping BWA-MEM 0.7.15 util sort
# ******************************************
SENTIEON_VERSION=$($SENTIEON_INSTALL_DIR/bin/sentieon driver --version)
if (( $(echo "${SENTIEON_VERSION##*-} < 201911" |bc -l) )); then
        ( $SENTIEON_INSTALL_DIR/bin/sentieon bwa mem -R "@RG\tID:$RGID\tSM:$SM\tPL:$PL" -t $NT \
            -K 100000000 -Y $FASTA $FASTQ_1 $FASTQ_2 || { echo -n 'bwa error'; exit 1; } ) | \
            ( $SAMBLASTER --addMateTags -a || { echo -n 'samblaster error'; exit 1; } ) | \
        $SENTIEON_INSTALL_DIR/bin/sentieon util sort -r $FASTA -o sorted.bam -t $NT --sam2bam -i -
else
        #Sentieon 201911 and higher use BWA 0.7.17, which already produce MC tags in the output
        ( $SENTIEON_INSTALL_DIR/bin/sentieon bwa mem -R "@RG\tID:$RGID\tSM:$SM\tPL:$PL" -t $NT \
            -K 100000000 -Y $FASTA $FASTQ_1 $FASTQ_2 || { echo -n 'error'; exit 1; } ) | \
        $SENTIEON_INSTALL_DIR/bin/sentieon util sort -r $FASTA -o sorted.bam -t $NT --sam2bam -i -
fi

# ******************************************
# 2. Mark Duplicates with Sentieon
# ******************************************
$SENTIEON_INSTALL_DIR/bin/sentieon driver -t $NT -i sorted.bam --algo LocusCollector \
    --fun score_info score.txt || { echo "LocusCollector failed"; exit 1; }

$SENTIEON_INSTALL_DIR/bin/sentieon driver -t $NT -i sorted.bam --algo Dedup --score_info score.txt \
   --metrics mark_dup_metrics.txt --output_dup_read_name tmp_dup_qname.txt || \
   { echo "Dedup1 failed"; exit 1; }

$SENTIEON_INSTALL_DIR/bin/sentieon driver -t $NT -i sorted.bam --algo Dedup \
   --dup_read_name tmp_dup_qname.txt markduped.bam || { echo "Dedup2 failed"; exit 1; }

# ******************************************
# 3. Base Quality Score Recalibration with Sentieon
# ******************************************
interval_arg="--interval chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,\
chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22"
$SENTIEON_INSTALL_DIR/bin/sentieon driver $interval_arg -r $FASTA -t $NT -i markduped.bam \
   --algo QualCal -k $KNOWN_MILLS -k $KNOWN_INDELS -k $KNOWN_DBSNP recal_data.table || \
   { echo "QualCal failed"; exit 1; }

$SENTIEON_INSTALL_DIR/bin/sentieon driver -r $FASTA -t $NT -i markduped.bam \
   --read_filter QualCalFilter,table=recal_data.table,prior=-1.0,indel=false,levels=10/20/30,min_qual=6 \
   --algo ReadWriter recaled_RW.cram || { echo "ReadWriter failed"; exit 1; }

# ******************************************
# 4. Haplotyper with Sentieon
# ******************************************
$SENTIEON_INSTALL_DIR/bin/sentieon driver -r $FASTA -t $NT -i recaled_RW.cram --algo Haplotyper \
    Haplotyper.vcf.gz || { echo "Haplotyper failed"; exit 1; }