Improvement: Downgrade GATK version

[schorlton]

Issue: Working with GATK 3.8 is a hassle. It requires download the jar and registering it separately due to licensing issues. This limits the ease of installation and distribution of MTBseq.

Solution: Downgrade the required version to GATK-lite 2.3.9. This is the last version of GATK released under a free for distribution license. It has pretty much the same functionality as version 3.8. There is a conda package available for it: https://anaconda.org/faircloth-lab/gatk-lite

Limitations: GATK 2.3.9 does not support indel searching in BaseRecalibrator. This can easily be disabled in TBrefine with flag --disable_indel_quals. I made few other changes to make it work. The java version would also have to be downgraded to 1.7.

Summary: I've activated a conda environment and made the above changes. MTBseq produces the exact same results.