Quick Start

The simplest way to load haplotypes from whole genome sequence (WGS : fastq, BAM, or GVCF) is to use the PopulatePHGDBPipelinePlugin. The parameter descriptions in the details section provide information about how the parameters are used and which ones you will need to set. If your life is not complicated enough or you need more control over the process, you can run the scripts used by this plugin on your own as described in Details.

Details

The scripts used by the plugin and distributed as part of the PHG Docker are CreateHaplotypesFromFastq.groovy, CreateHaplotypesFromBAM.groovy, and CreateHaplotypesFromGVCF.groovy. These scripts can also be found in the PHG source code repository.

To align sequence from fastq files to the reference genome and load the resulting haplotypes to the database, use the script CreateHaplotypesFromFastq.groovy. This script aligns the reads to created BAM files then calls CreateHaplotypesFromBAM.groovy, which in turn calls CreateHaplotypesFromGVCF.groovy. To start with BAM files run CreateHaplotypesFromBAM.groovy. To start with GVCF files, run CreateHaplotypesFromGVCF.groovy

Because the BAM files can be quite large, you may wish to delete them after the GVCFs are created. Saving the GVCFs is worthwhile should it be necessary to rebuild the database.

Sentieon

Sentieon is a commercial version of GATK that runs much faster. By default, GATK HaplotypeCaller is used to call variants from BAM files. If a Sentieon license is provided in the config file, Sentieon will be used.

Parameters

The following are parameters that can or be assigned in the config file. Some of the parameters are required and do not have default values. The default paths will work with the Docker PHG when the MakeDefaultDirectory plugin is used to create a directory structure. Running CreateHaplotypesFromFastq.groovy uses all of the parameters. Running CreateHaplotypesFromBAM.groovy uses parameters for that script plus CreateHaplotypesFromGVCF.groovy. Running CreateHaplotypesFromGVCF.groovy uses only CreateHaplotypesFromGVCF parameters.

CreateHaplotypesFromFastq.groovy

Name	Default	Description
referenceFasta	required	full path to the reference fasta file
wgsKeyFile	required	the key file listing the fastq's to be processed
numThreads	10	the maximum number of threads to be used
picardPath	/picard.jar	The path to picard.jar
fastqFileDir	/phg/inputDir/loadDB/fastq/	the directory holding the fastq files
tempFileDir	/phg/inputDir/loadDB/temp/	the storage location for temporary files created by the script
dedupedBamDir	/phg/inputDir/loadDB/bam/dedup/	the stroace location for the deduped BAM files created by the script

CreateHaplotypesFromBAM.groovy

Name	Default	Description
referenceFasta	required	full path to the reference fasta file
numThreads	10	the maximum number of threads to be used
gvcfFileDir	/phg/inputDir/loadDB/gvcf/	directory where gvcf files will be written
tempFileDir	/phg/inputDir/loadDB/bam/temp/	directory where temporary files will be written
filteredBamDir	/phg/inputDir/loadDB/bam/mapqFiltered/	directory where filtered BAMs will be written
dedupedBamDir	/phg/inputDir/loadDB/bam/dedup/	directory where deduped BAMs will be written
Xmx	10G	Max Java Heap Space used when running TASSEL code
extendedWindowSize	1000	adds flanking regions (base pairs) to reference ranges for BAM filtering
tasselLocation	/tassel-5-standalone/run_pipeline.pl	location of TASSEL, default works for docker
mapQ	48	minimum MapQ value used in the BAM file filtering
sentieon_license	optional	the sentieon license if you have one
sentieonPath	/sentieon/bin/sentieon	the path to the Sentieon executable
gatkPath	/gatk/gatk	the path to the gatk executable

CreateHaplotypesFromGVCF.groovy

Name	Default	Description
refRangeMethods	refRegionGroup
tempFileDir	/phg/inputDir/loadDB/bam/temp/
tasselLocation	/tassel-5-standalone/run_pipeline.pl
extendedWindowSize	1000
Xmx	10G

Wiki

PracticalHaplotypeGraph / UserInstructions / CreatePHG_step2_addHaplotypesFromWGS