### Displaying Help for a Specific Algorithm

Source: https://support.sentieon.com/docs/usages/driver/driver

This example shows how to get help information for a particular algorithm supported by the DRIVER tool.

```bash
sentieon driver --algo ALGORITHM --help

```

--------------------------------

### Configure License Server with SysVinit

Source: https://support.sentieon.com/docs/examples/examples

Set up the Sentieon license server to start automatically on systems using traditional System V init scripts. This involves creating a configuration file and installing a startup script.

```bash
licsrvr="/home/sentieon/release/latest/bin/sentieon licsrvr"
licfile=/home/sentieon/licsrvr/licsrvr.lic
logfile=/home/sentieon/licsrvr/licsrvr.log

```

```bash
install -m 0755 $SENTIEON_INSTALL_DIR/doc/licsrvr.sh /etc/init.d/licsrvr

```

```bash
/usr/lib/lsb/install_initd /etc/init.d/licsrvr

```

```bash
chkconfig --add licsrvr
chkconfig licsrvr on

```

```bash
update-rc.d licsrvr defaults
update-rc.d licsrvr enable

```

```bash
service licsrvr [start|stop|restart|status]

```

--------------------------------

### Start Sentieon License Server

Source: https://support.sentieon.com/docs/quick_start

Run this command on the license server to start the license server process. Specify the log file and the path to the license file.

```bash
<SENTIEON_INSTALL_DIR>/bin/sentieon licsrvr --start --log LOG_FILE LICENSE_PATH/LICENSE_FILE

```

--------------------------------

### Install License Server Service File

Source: https://support.sentieon.com/docs/examples/examples

Installs the license server startup script to the systemd system directory. Ensure the SENTIEON_INSTALL_DIR environment variable is set correctly.

```bash
install -m 0644 $SENTIEON_INSTALL_DIR/doc/licsrvr.service /etc/systemd/system
```

--------------------------------

### Example Readgroup Argument

Source: https://support.sentieon.com/docs/sentieon_cli

This is an example of the readgroup information format required for FASTQ input.

```bash
--readgroups "@RG\tID:HG002-1\tSM:HG002\tLB:HG002-LB-1\tPL:ILLUMINA"
```

--------------------------------

### Unpack Quick Start Package

Source: https://support.sentieon.com/docs/quick_start

Extract the Sentieon quick start package, which contains sample data and scripts for testing.

```bash
tar xzvf sentieon_quickstart.tar.gz
```

--------------------------------

### Start Sentieon License Server

Source: https://support.sentieon.com/docs/introduction/intro

Start the Sentieon license server process, providing the directory where license files are stored. This is necessary if you are using a license server.

```bash
<SENTIEON_FOLDER>/bin/sentieon licsrvr --start LICENSE_DIR/LICENSE_FILE.lic

```

--------------------------------

### Launch Sentieon Quick Start Script

Source: https://support.sentieon.com/docs/quick_start

Execute the main Sentieon quick start script in the background. The entire run typically takes 3-5 minutes.

```shell
sh sentieon_quickstart.sh &

```

--------------------------------

### Sentieon QualityYield Command Line

Source: https://support.sentieon.com/docs/appnotes/arguments

Example of running the Sentieon QualityYield algorithm.

```bash
sentieon driver -t NUMBER_THREADS -r REFERENCE.FASTA \
   -i DEDUPED.BAM --algo QualityYield \
   YIELD_METRICS.TXT

```

--------------------------------

### Start Sentieon License Server

Source: https://support.sentieon.com/docs/appnotes/azure_deployment

Command to start the Sentieon license server on a Standard_B1s instance. Ensure a port above 1024 is used for non-root execution.

```bash
sentieon licsrvr --start [-l <licsrvr_log>] <license_file>
```

--------------------------------

### Enable Automatic License Server Start

Source: https://support.sentieon.com/docs/examples/examples

Enables the license server service to start automatically on system boot. This command should be run as root.

```bash
systemctl enable licsrvr.service
```

--------------------------------

### Sentieon WgsMetricsAlgo Command Line

Source: https://support.sentieon.com/docs/appnotes/arguments

Example of running the Sentieon WgsMetricsAlgo algorithm.

```bash
sentieon driver -t NUMBER_THREADS -r REFERENCE.FASTA \
   -i DEDUPED.BAM --algo WgsMetricsAlgo \
   WGS_METRICS.TXT

```

--------------------------------

### Start License Server with Authentication Script

Source: https://support.sentieon.com/docs/appnotes/license_server

Launch the license server with the --auth option pointing to your custom authentication script.

```bash
sentieon licsrvr --start --auth /path/to/auth.py /path/to/licfile

```

--------------------------------

### Install jemalloc on Ubuntu 20.04

Source: https://support.sentieon.com/docs/appnotes/jemalloc

Use these commands to update package lists and install `libjemalloc2` on Ubuntu 20.04 systems.

```bash
apt update
apt install libjemalloc2
```

--------------------------------

### Sentieon SequenceArtifactMetricsAlgo Command Line

Source: https://support.sentieon.com/docs/appnotes/arguments

Example of running the Sentieon SequenceArtifactMetricsAlgo algorithm.

```bash
sentieon driver -t NUMBER_THREADS -r REFERENCE.FASTA \
   -i DEDUPED.BAM --algo SequenceArtifactMetricsAlgo \
   --dbsnp DBSNP.VCF ARTIFACT_METRICS_BASE

```

--------------------------------

### Start or Stop LICSRVR Binary

Source: https://support.sentieon.com/docs/usages/licsrvr/licsrvr

Use this command to start or stop the Sentieon license server. Specify the log file location and the license file path.

```bash
<SENTIEON_FOLDER>/bin/sentieon licsrvr [--start|--stop] [--log LOG_FILE] LICENSE_FILE
```

--------------------------------

### TNhaplotyper2 and TNfilter Command Example

Source: https://support.sentieon.com/docs/appnotes/out_fields

Example command for running TNhaplotyper2 to call somatic variants and TNfilter to refine the calls. Ensure to replace placeholders with actual file paths and sample names.

```bash
sentieon driver -t NUMBER_THREADS -r REFERENCE.FASTA \
   -i NORMAL_RECALED.BAM -i TUMOR_RECALED.BAM \
   --algo TNhaplotyper2 --tumor_sample TUMOR_SM \
   --normal_sample NORMAL_SM \
   TMP.VCF \
   --algo OrientationBias --tumor_sample TUMOR_SM \
   ORIENTATION_DATA \
   --algo ContaminationModel --tumor_sample TUMOR_SM \
   --normal_sample NORMAL_SM \
   --vcf GERMLINE_RESOURCE \
   --tumor_segments CONTAMINATION_DATA.segments \
   CONTAMINATION_DATA

sentieon driver -r REFERENCE.FASTA \
   --algo TNfilter --tumor_sample TUMOR_SM \
   --normal_sample NORMAL_SM \
   -v TMP.VCF \
   --contamination CONTAMINATION_DATA \
   --tumor_segments CONTAMINATION_DATA.segments \
   --orientation_priors ORIENTATION_DATA \
   OUTPUT.VCF

```

--------------------------------

### Install jemalloc on RHEL/CentOS 8.x

Source: https://support.sentieon.com/docs/appnotes/jemalloc

Use these commands to install jemalloc and its dependencies on RHEL/CentOS 8.x systems.

```bash
yum install epel-release
yum install jemalloc
```

--------------------------------

### Configure Sentieon Quick Start Script

Source: https://support.sentieon.com/docs/quick_start

Edit the 'sentieon_quickstart.sh' script to set essential environment variables and parameters before execution.

```bash
# Update with the location of the Sentieon software package
SENTIEON_INSTALL_DIR=/home/release/sentieon-genomics-202503.03

# Update with the location of temporary fast storage and uncomment
#SENTIEON_TMPDIR=/tmp

# It is important to assign meaningful names in actual cases.
# It is particularly important to assign different read group names.
sample="sample_name"
group="read_group_name"
platform="ILLUMINA"

# Other settings
nt=16 #number of threads to use in computation

```

--------------------------------

### Applying Read Filters

Source: https://support.sentieon.com/docs/usages/driver/driver

This example demonstrates how to apply a read filter before the algorithm processes the reads.

```bash
sentieon driver -r ref.fasta -i input.bam --read_filter "FILTER,OPTION=VALUE" --algo ALGORITHM ...

```

--------------------------------

### Picard CollectQualityYieldMetrics Command Line

Source: https://support.sentieon.com/docs/appnotes/arguments

Example of running the Picard CollectQualityYieldMetrics command.

```bash
java -jar picard.jar CollectQualityYieldMetrics \
   I=DEDUPED.BAM O=YIELD_METRICS.TXT

```

--------------------------------

### Install jemalloc on Ubuntu 18.04

Source: https://support.sentieon.com/docs/appnotes/jemalloc

Use these commands to update package lists and install `libjemalloc1` on Ubuntu 18.04 systems.

```bash
apt update
apt install libjemalloc1
```

--------------------------------

### Example Python License Server Extension Script

Source: https://support.sentieon.com/docs/appnotes/license_server

An example Python script for the license server extension that parses JSON input and performs authentication checks. It returns 0 on success and non-zero on failure.

```python
#!/usr/bin/env python
import json
import sys
import urllib

secret_key = “My_scret_key”

def main(argv):
    inputs = json.load(sys.stdin)
    print >>sys.stderr, inputs
    if inputs.get('mech') != 'unix':
        print >>sys.stderr, "mech not unix"
        return -1
    if inputs.get('data') != secret_key:
        print >>sys.stderr, "Incorrect key"
        return -1
    if not isinstance(inputs.get('groups'), list):
        return -1
    if 'Developers' not in inputs.get('groups'):
        print >>sys.stderr, "Developers not in groups"
        return -1
    if 'baduser' == inputs.get('user'):
        print >>sys.stderr, "baduser is running the test"

    return 0

if __name__ == '__main__':
    sys.exit(main(sys.argv))

```

--------------------------------

### GATK3 ContEst Command Line

Source: https://support.sentieon.com/docs/appnotes/arguments

Example of how to run the GATK3 ContEst tool. Ensure GenomeAnalysisTK.jar is in your PATH or specify its full path.

```bash
java -jar GenomeAnalysisTK.jar -T ContEst -I TUMOR_RECALED.BAM \
   -R REFERENCE.FASTA -pf POPULATION.VCF --genotypes GENOTYPES.VCF \
   -o OUTPUT.TXT

```

--------------------------------

### Picard ConvertSequencingArtifactToOxoG Command Line

Source: https://support.sentieon.com/docs/appnotes/arguments

Example of running the Picard ConvertSequencingArtifactToOxoG command.

```bash
java -jar picard.jar ConvertSequencingArtifactToOxoG \
   I=DEDUPED.BAM O=ARTIFACT_METRICS_BASE R=REFERENCE.FASTA \
   OUTPUT_BASE=oxog_metrics

```

--------------------------------

### Picard CollectSequencingArtifactMetrics Command Line

Source: https://support.sentieon.com/docs/appnotes/arguments

Example of running the Picard CollectSequencingArtifactMetrics command.

```bash
java -jar picard.jar CollectSequencingArtifactMetrics \
   I=DEDUPED.BAM O=ARTIFACT_METRICS_BASE R=REFERENCE.FASTA \
   DB_SNP=DBSNP.VCF

```

--------------------------------

### Picard CollectWgsMetrics Command Line

Source: https://support.sentieon.com/docs/appnotes/arguments

Example of running the Picard CollectWgsMetrics command.

```bash
java -jar picard.jar CollectWgsMetrics \
   I=DEDUPED.BAM O=WGS_METRICS.TXT R=REFERENCE.FASTA

```

--------------------------------

### Specifying Temporary Directory

Source: https://support.sentieon.com/docs/usages/driver/driver

This example shows how to set a custom directory for temporary files generated during processing.

```bash
sentieon driver -r ref.fasta -i input.bam --temp_dir /path/to/temp --algo ALGORITHM ...

```

--------------------------------

### Adding Padding to Intervals

Source: https://support.sentieon.com/docs/usages/driver/driver

This example shows how to add padding to the specified intervals to extend their boundaries.

```bash
sentieon driver -r ref.fasta -i input.bam --interval interval.bed --interval_padding 100 --algo ALGORITHM ...

```

--------------------------------

### Sentieon ContaminationAssessment Command Line

Source: https://support.sentieon.com/docs/appnotes/arguments

Example of how to run the Sentieon ContaminationAssessment tool. This command uses the 'driver' utility for execution.

```bash
sentieon driver -t NUMBER_THREADS -r REFERENCE.FASTA -i TUMOR_RECALED.BAM \
   --algo ContaminationAssessment --pop_vcf POPULATION.VCF \
   --genotype_vcf GENOTYPES.VCF OUTPUT.TXT

```

--------------------------------

### Specifying Input Intervals with a BED File

Source: https://support.sentieon.com/docs/usages/driver/driver

This example shows how to use a BED file to define the genomic intervals for processing.

```bash
sentieon driver -r ref.fasta -i input.bam --interval interval.bed --algo ALGORITHM ...

```

--------------------------------

### Download Terraform Configuration Files

Source: https://support.sentieon.com/docs/appnotes/aws_deployment

Clone the Sentieon Terraform configuration repository and navigate to the AWS license server directory. Ensure you have Git installed.

```bash
git clone https://github.com/sentieon/terraform
cd terraform/aws_license-server
```

--------------------------------

### Specifying Input Intervals with Picard Interval List

Source: https://support.sentieon.com/docs/usages/driver/driver

This example demonstrates using a Picard-formatted interval list file to define processing regions.

```bash
sentieon driver -r ref.fasta -i input.bam --interval interval_list.interval --algo ALGORITHM ...

```

--------------------------------

### Example JSON Payload Sent to License Server

Source: https://support.sentieon.com/docs/appnotes/license_server

This JSON string, containing authentication details and user information, is sent from the computing node to the license server when a job starts.

```json
{u'mech': u'METHOD', u'data': u'ASK_ME', u'addr': u'10.1.2.3',\nu'groups': [u'Domain Users', u'Developers'], u'user': u'goodguy'}

```

--------------------------------

### Install gnuplot Dependencies and Build on Ubuntu/Debian

Source: https://support.sentieon.com/docs/appnotes/gnuplot

Installs required packages, downloads, configures, and builds gnuplot from source. May require sudo privileges for package installation and final installation.

```bash
apt update  # may require sudo
apt install make gcc gzip libgd-dev libcairo2-dev libpango1.0-dev curl  # may require sudo
curl -L "https://downloads.sourceforge.net/project/gnuplot/gnuplot/6.0.2/gnuplot-6.0.2.tar.gz" | \
  tar -zxf -
cd gnuplot-6.0.2
./configure
make
make install  # may require sudo

```

--------------------------------

### Install gnuplot Dependencies and Build on Rocky Linux/AlmaLinux

Source: https://support.sentieon.com/docs/appnotes/gnuplot

Installs necessary development tools and libraries, downloads, configures, and builds gnuplot from source. May require sudo privileges for package installation and final installation.

```bash
yum install gcc make patch gzip tar cairo-devel pango-devel  # may require sudo
curl -L "https://downloads.sourceforge.net/project/gnuplot/gnuplot/6.0.2/gnuplot-6.0.2.tar.gz" | \
  tar -zxf -
cd gnuplot-6.0.2
./configure
make
make install  # may require sudo

```

--------------------------------

### Example: Running Multiple Algorithms

Source: https://support.sentieon.com/docs/usages/driver/driver

Demonstrates how to execute multiple algorithms within a single DRIVER call, where OPTIONS are shared across all specified algorithms.

```bash
sentieon driver [shared OPTIONS] \
--algo ALGORITHM1 ALGO_OPTION1 OUTPUT1 \
--algo ALGORITHM2 ALGO_OPTION2 OUTPUT2

```

--------------------------------

### Default jemalloc library path on Ubuntu 18.04

Source: https://support.sentieon.com/docs/appnotes/jemalloc

This is the default installation path for `libjemalloc.so.1` on Ubuntu 18.04 after installation.

```bash
/usr/lib/x86_64-linux-gnu/libjemalloc.so.1
```

--------------------------------

### Default jemalloc library path on Ubuntu 20.04

Source: https://support.sentieon.com/docs/appnotes/jemalloc

This is the default installation path for `libjemalloc.so.2` on Ubuntu 20.04 after installation.

```bash
/usr/lib/x86_64-linux-gnu/libjemalloc.so.2
```

--------------------------------

### Default jemalloc library path on RHEL/CentOS 7.x

Source: https://support.sentieon.com/docs/appnotes/jemalloc

This is the default installation path for `libjemalloc.so.1` on RHEL/CentOS 7.x after installation.

```bash
/usr/lib64/libjemalloc.so.1
```

--------------------------------

### Default jemalloc library path on RHEL/CentOS 8.x

Source: https://support.sentieon.com/docs/appnotes/jemalloc

This is the default installation path for `libjemalloc.so.2` on RHEL/CentOS 8.x after installation.

```bash
/usr/lib64/libjemalloc.so.2
```

--------------------------------

### Set Up Cluster License Environment Variable

Source: https://support.sentieon.com/docs/quick_start

After confirming connectivity, set this environment variable on computing nodes to use the cluster license server.

```bash
export SENTIEON_LICENSE=LICSRVR_HOST:LICSRVR_PORT

```

--------------------------------

### General DRIVER Command Syntax

Source: https://support.sentieon.com/docs/usages/driver/driver

This is the basic structure for running the DRIVER binary. It shows how to specify options, algorithms, and their respective outputs.

```bash
sentieon driver OPTIONS --algo ALGORITHM ALGO_OPTION OUTPUT \
[--algo ALGORITHM2 ALGO_OPTION2 OUTPUT2]

```

--------------------------------

### Example TNsnv Command

Source: https://support.sentieon.com/docs/appnotes/out_fields

This command demonstrates how to run the TNsnv algorithm, specifying input files, reference genome, intervals, and various output file configurations.

```bash
sentieon driver -t NUMBER_THREDS -r REFERENCE.FASTA \
   -i NORMAL_RECALED.BAM -i TUMOR_RECALED.BAM \
   --interval INTERVAL \
   --algo TNsnv --dbsnp DBSNP.VCF \
   --tumor_sample TUMOR_SM --normal_sample NORMAL_SM \
   -call_stats_out CALL_STATS_OUTPUT.TXT
   --stdcov_out STD_COVERAGE.TXT \
     Standard coverage output file
   --q20cov_out Q20_COVERAGE.TXT \
     Q20 coverage output file
   --power_out POWER.TXT --tumor_depth_out TUMOR_DP.TXT \
   --normal_depth_out NORMAL_DP.TXT OUTPUT.VCF

```

--------------------------------

### Manually Start and Stop License Server Service

Source: https://support.sentieon.com/docs/examples/examples

Provides commands to manually start and stop the Sentieon license server service using systemctl. These commands require root privileges.

```bash
systemctl start licsrvr.service
```

```bash
systemctl stop licsrvr.service
```

--------------------------------

### Sample Group Configuration File

Source: https://support.sentieon.com/docs/appnotes/distributed_mode

Define sample groups for splitting by creating a tab-separated file. Each line specifies an output file and the samples belonging to that group.

```text
GVCFtyper_file_group1.vcf.gz Sample1 Sample2 Sample3
GVCFtyper_file_group1.vcf.gz Sample4 Sample5
GVCFtyper_file_group2.vcf.gz Sample6 Sample7 Sample8

```

--------------------------------

### Distributed BWA Mapping Setup

Source: https://support.sentieon.com/docs/appnotes/distributed_mode

Shell script setup for distributed BWA mapping, defining input files and parameters. It calculates the number of runs based on input size and desired server count.

```bash
# Sample file for distributing DNAseq pipeline onto 4 1GBase shards
# Each stage command can be distributed to a different server for faster processing,
# but the user needs to make sure that the necessary files are present in each machine

FASTA="/home/b37/human_g1k_v37_decoy.fasta"
FASTQ_1="WGS-30x_1.fastq.gz"
FASTQ_2="WGS-30x_2.fastq.gz"
FASTQ_INDEX="WGS-30x.fastq.gz.index"
KNOWN1="/home/b37/1000G_phase1.indels.b37.vcf.gz"
KNOWN2="/home/b37/Mills_and_1000G_gold_standard.indels.b37.vcf.gz"
DBSNP="/home/b37/dbsnp_138.b37.vcf.gz"

#######################################
# BWA mapping, distributed on 4 servers
#######################################
BWA_K_size=100000000
num_srvr=4

#get the number of runs that the inputs will be split into given the size
num_K=$(sentieon fqidx query -i $FASTQ_INDEX | cut -d' ' -f1)
BWA_K_size=$(sentieon fqidx query -i $FASTQ_INDEX | cut -d' ' -f2)
num_K_srvr=$(expr $num_K / $num_srvr + 1)
```

--------------------------------

### GATK4 Mutect2 Best Practices Workflow

Source: https://support.sentieon.com/docs/appnotes/arguments

This snippet shows the GATK4 best practices command line for running Mutect2, including steps for pileup summaries, orientation model learning, contamination calculation, and filtering.

```bash
gatk Mutect2 -R REFERENCE.FASTA -I TUMOR_RECALED.BAM \
   -tumor TUMOR_SM -I NORMAL_RECALED.BAM -normal NORMAL_SM \
   --germline-resource GNOMAD.VCF -O TMP.VCF \
   --f1r2-tar-gz F1R2.TAR.GZ -L INTERVAL
gatk GetPileupSummaries -R REFERENCE.FASTA -I TUMOR_RECALED.BAM \
   -V GNOMAD.VCF -O TUMOR.PILEUPS -L INTERVAL
gatk GetPileupSummaries -R REFERENCE.FASTA -I NORMAL_RECALED.BAM \
   -V GNOMAD.VCF -O NORMAL.PILEUPS -L INTERVAL
gatk LearnReadOrientationModel -I F1R2.TAR.GZ -O PRIORS
gatk CalculateContamination -I TUMOR.PILEUPS \
   -matched NORMAL.PILEUPS --tumor-segmentation SEGMENTS \
   -O CONTAMINATION.TABLE
gatk FilterMutectCalls -V TMP.VCF -R REFERENCE.FASTA \
   -O OUTPUT.VCF --contamination-table CONTAMINATION.TABLE \
   --tumor-segmentation SEGMENTS -ob-priors PRIORS \
   --stats TMP.VCF.stats --filtering-stats OUTPUT.VCF.stats

```

--------------------------------

### UMI Binary General Syntax

Source: https://support.sentieon.com/docs/usages/umi/umi

The general syntax for invoking the UMI binary. This is the entry point for all UMI operations.

```bash
sentieon umi MODE [OPTIONS]
```

--------------------------------

### TNHaplotyper Driver Command

Source: https://support.sentieon.com/docs/appnotes/out_fields

Example command to run the TNhaplotyper algorithm. Ensure you replace placeholders like NUMBER_THREADS, REFERENCE.FASTA, BAM files, INTERVAL, DBSNP.VCF, and sample names with your specific values.

```bash
sentieon driver -t NUMBER_THREADS -r REFERENCE.FASTA \
   -i NORMAL_RECALED.BAM -i TUMOR_RECALED.BAM \
   --interval INTERVAL \
   --algo TNhaplotyper --dbsnp DBSNP.VCF \
   --tumor_sample TUMOR_SM --normal_sample NORMAL_SM \
   OUTPUT.VCF

```

--------------------------------

### Provision Sentieon License Server Infrastructure

Source: https://support.sentieon.com/docs/appnotes/aws_deployment

Use this command to provision the necessary AWS infrastructure for the Sentieon license server. Ensure you replace placeholders with your specific values.

```bash
terraform apply \
  -var 'aws_region=<AWS_REGION>' \
  -var 'licsrvr_fqdn=<FQDN>' \
  -var 'license_s3_uri=s3://<S3_URI>'
```

--------------------------------

### Sentieon AlignmentStat Command Line

Source: https://support.sentieon.com/docs/appnotes/arguments

Example command for running AlignmentStat in Sentieon. Requires input BAM, output file, reference FASTA, adapter sequence, and thread count.

```bash
sentieon driver -t NUMBER_THREADS -r REFERENCE.FASTA \
   -i ALIGNED.BAM --algo AlignmentStat \
   --adapter_seq ADAPTERS_SEQ ALN_METRICS.TXT

```

--------------------------------

### Sentieon BaseDistributionByCycle Command Line

Source: https://support.sentieon.com/docs/appnotes/arguments

Example command for running BaseDistributionByCycle in Sentieon. Requires input BAM, output metrics file, reference FASTA, and thread count.

```bash
sentieon driver -t NUMBER_THREADS -r REFERENCE.FASTA \
   -i ALIGNED.BAM --algo BaseDistributionByCycle \
   BASE_DISTRIBUTION_METRICS.TXT

```

--------------------------------

### Check Python Version

Source: https://support.sentieon.com/docs/quick_start

Verify the installed Python version on your system. This is a prerequisite for Sentieon software.

```bash
python --version
```

--------------------------------

### GATK Best Practices Alignment and Sorting

Source: https://support.sentieon.com/docs/appnotes/arguments

This snippet shows the command-line execution for alignment using BWA and subsequent sorting and indexing using Picard and samtools, following GATK Best Practices.

```bash
bwa mem -M -R '@RG\tID:GROUP_NAME \tSM:SAMPLE_NAME \tPL:PLATFORM' -p \
   -t NUMBER_THREADS REFERENCE.FASTA SAMPLE.FQ > ALIGNED.SAM
java -jar picard.jar SortSam INPUT=ALIGNED.SAM \
   OUTPUT=SORTED.SAM SORT_ORDER=coordinate
samtools view -bS SORTED.SAM > SORTED.BAM
samtools index SORTED.BAM

```

--------------------------------

### Skipping Unmapped Reads

Source: https://support.sentieon.com/docs/usages/driver/driver

This example demonstrates how to configure the driver to skip unmapped reads during processing.

```bash
sentieon driver -r ref.fasta -i input.bam --skip_no_coor --algo ALGORITHM ...

```

--------------------------------

### QualCalFilter with Table Input

Source: https://support.sentieon.com/docs/usages/driver/driver

Example of using the QualCalFilter read filter with a specified recalibration table file.

```bash
--read_filter QualCalFilter,table=$TABLE_FILEPATH
```

--------------------------------

### Load jemalloc using LD_PRELOAD for Sentieon applications

Source: https://support.sentieon.com/docs/appnotes/jemalloc

Set the `LD_PRELOAD` environment variable to load the jemalloc library at runtime for Sentieon tools, using the appropriate path for your system.

```bash
export LD_PRELOAD=/usr/lib64/libjemalloc.so.2
```