First versions. Working
Updated to only create a working directory if running in array mode. Added readlink for RefFil. Added filter to GATK to remove reads with mismatched base and quality score numbers rather than blowing up (see GATK documentation).
Added \"kill switch\" flag to ExmAln.6 to allow it to be used without removing the original file. Added the necessary -K flag to ExmAln.5 call the removal when using the pipeline. Added readlink for RefFil.
Added readlink for RefFil. Few other minor changes.
Tweaks to script to get pipeline running smoothly. Added readlink for RefFil.
Added hard filtering. Tweaks to script to get pipeline running smoothly. Added readlink for RefFil.
Added line to get vcf stats. Change Mut to Var in the INFO ids. Tweaks to script to get pipeline running smoothly. Added readlink for RefFil.
Updated for new annotation flags.
Changed error checking function.
Fixed bad path to target intervals file.
New file for updating GATK annotations in a vcf. Functional
New reference file for testing the nightly GATK build
Various minor cosmetic changes, mostly updates to comments
Added option to get GATK to fix pre-1.8 quality scores to 1b. Added options to call just the BamMetrics and not the whole pipeline after AdHoc.2. Various minor cosmetic changes, mostly updates to comments
Various minor streamlining changes. Updates to commnents
Further development, now basically functional
Fixed the check for the HaplotypeCaller. Updates to commnents
Updated to account for multiple alternate alleles