Just noticed that SelectVariants produces "ERROR MESSAGE: Invalid argument value '>' at position 10" when I use the '-select' parameter with the syntax given in your third example [-select "QD > 10.0"]. I'm using GATK 2.6-5, java/1.7.0_25. It worked well without the whitespace in the expression [-select "QD>10.0"]. Hope that's not just me ;-) Also, does the example miss the line continuation character just before the '-select' option?
No worries, many thanks for the great tool!