SAM_Processing

Basic Usage

The SAM_Processing handler sorts, de-duplicates, adds read groups to, and merges the SAM files produced from Read_Mapping into one finished BAM file. This script utilizes Picard to carry out all processing of the SAM files. In addition, it creates before and after statistics using the flagstat function of SAMTools. To run SAM_Processing, all common variables and handler-specific variables must be defined within the config file. Once the variables have been defined, SAM_Processing can be run with the following command:

sequence_handling SAM_Processing Config

Where Config is the full file path to the configuration file.

Future features: After the job has run, a list of sorted, deduplicated, and read grouped BAM files will be generated in addition to the merged BAM file.

Handler-Specific Variables

The following are a list of variables that need to be defined within Config. In addition to the handler-specific variables, all common variables must be defined.

Variable	Function	Method
METHOD	Which program should be used to process the SAM files. Choose from 'picard' (recommended) or 'samtools'.	Picard and SAMtools
SP_QSUB	QSub settings for batch submission. Recommended settings are "mem=12gb,nodes=1:ppn=8,walltime=24:00:00".	Picard and SAMtools
MAPPED_DIRECTORY	The full file path to the directory containing the read-mapped samples. If using Read_Mapping then leave as "${OUT_DIR}/Read_Mapping".	Picard and SAMtools
PICARD_JAR	The full file path for the Picard jar file.	Picard
MAX_MEM	The most amount of memory that can be used, formatted like 15g.	Picard
MAX_FILES	The maximum number of file handles that can be used. For UNIX systems, the per-process maximum number of files that can be open may be found with ulimit -n. Set slightly under this value.	Picard
TMP	An optional variable that tells Picard where to store temporary files. Only use if you've had issues running out of temp space. Otherwise, leave blank.	Picard

Output

SAM_Processing creates sorted, deduplicated BAM files that have read groups marked. In addition, it also generates a merged BAM file for other tasks such as variant calling, alignment statistics for all input SAM files, and the finished unmerged BAM files. Finally, a list of all finished unmerged BAM files is generated.

Dependencies

SAM_Processing depends on Picard and Java 1.8 for all processing needs as well as SAMTools 1.3.1 for generating the alignment statistics. In addition, PBS and GNU Parallel are required for basic running.

Next: Coverage_Mapping