Legacy Documentation - PHG Version 1
This section contains documentation for PHG version 1, which is no longer actively developed. It is preserved here for archival and historical reference only. If you are looking to use the Practical Haplotype Graph, please refer to the PHG v2 documentation, which reflects the current version of the software.
SAMToMappingPlugin¶
Overview¶
This plugin allows you to create ReadMappings from an existing SAM/BAM file and upload them to the DB. This uses a KeyFile similarly to FastqToMappingPlugin, but will skip the Minimap2 Alignment step.
Steps:¶
- Loop through each SAM file in the key file
- Apply a set of filters to the mappings
- Push the readMapping to the DB
- Generate a Path KeyFile for use with Path finding.
Example Run Command¶
#!bash
time /tassel-5-standalone/run_pipeline.pl -debug -Xmx100G -configParameters [CONFIG_FILE] -HaplotypeGraphBuilderPlugin -configFile [CONFIG_FILE] -methods [HAPLOTYPE_METHOD] -includeVariantContexts false -includeSequences false -endPlugin -SAMToMappingPlugin -endPlugin
Config Parameters¶
#!bash
SAMToMappingPlugin.keyFile = Name of the Keyfile to process. Must have columns cultivar, flowcell_lane, filename, and PlateID.
SAMToMappingPlugin.samDir = Name of the SAM/BAM dir to process.
SAMToMappingPlugin.maxRefRangeErr = Maximum allowed error when choosing best reference range to count. Error is computed 1 - (mostHitRefCount/totalHits)
SAMToMappingPlugin.lowMemMode = true(default) or false. If true, will run in a memory efficient manner with minimal performance hit. If the reads are not ordered in the SAM file, you must use false and the whole file must fit in RAM
SAMToMappingPlugin.methodName = Name of the ReadMappings to be stored in the DB.
SAMToMappingPlugin.methodDescription = Description of the method
SAMToMappingPlugin.debugDir = (Optional)Directory on the file system that will write the ReadMapping files to disk.
SAMToMappingPlugin.outputSecondaryStats = True or false(default). If true this will out put some additional mapping statistics which can be used to debug. The files will be written to the current working directory.