Switched ExmAln.4 back to using whole chromosome as this was just as quick as using a target file subset and tidier. Tidied up some file names and if statements. Couple of minor bug fixes.
Tidied up if statement syntax
Adjustment to ExmAln4 to allow for either running per chromosome or across entire exome - need to use different target (-L) for GATK in each case. Added the ArrNum to variable to all the others for consistency. Some other minor syntax changes.
Added CADD annotation. Also, fixed unwanted spaces and semi-colons in the annotations.
Added SureSelect v5 target code
Update to Target code function and change to ArrNum variable
New scripts. Mostly functional
First draft of new UG script. Working.
First draft of new Merge script for UG data. Working
Some minor changes to output filenames etc.
Changed the ID names for the annotations to be added to the INFO field
Added a lines for VCF names to the log
Added new capture kit codes
First draft of new VQSR script. Working