Removed multithreading from GenBQSR
minor change to usage
Fixed the if/else conditions for calling the next step. Removed the multithreading. Adjusted the names of various temporary files. Removed the -L argument from GATK as it is not necessary as this is a read walker - it just means that GATK cannot accurately predict the total time the job will take
Mostly changes to comments. Couple of minor bugs.
First iteration of working script.
Added Error message output to logging on failed job
Starting points - non-working
Increase time allocation
Annotate now works with latest annovar.
Added new function to allow a code to be used instead of the target intervals file location. Codes are contained in the reference file
renamed reference file
Adjusted scripts to allow the realignment/recalibration process to be run either over entire bam in a single pass or split across chromosomes. Also added function to find target intervals files by codes. Also added intervals to the realignment phase to speed things up a little.
Added intervals to GATK command
Fixed qstat command for array jobs
Fixed gVCF output name, and added log to GATK command