LICENSE.txt
MANIFEST.in
README.rst
setup.py
mitopipeline/__init__.py
mitopipeline/cmdline.py
mitopipeline/cmdline_parser.py
mitopipeline/config.py
mitopipeline/downloader.py
mitopipeline/logging.py
mitopipeline/pipeline_builder.py
mitopipeline/pipeline_runner.py
mitopipeline/templates.py
mitopipeline/util.py
mitopipeline.egg-info/PKG-INFO
mitopipeline.egg-info/SOURCES.txt
mitopipeline.egg-info/dependency_links.txt
mitopipeline.egg-info/entry_points.txt
mitopipeline.egg-info/requires.txt
mitopipeline.egg-info/top_level.txt
mitopipeline/steps/annovar.sh
mitopipeline/steps/clipping.sh
mitopipeline/steps/downsample.sh
mitopipeline/steps/extractmito.sh
mitopipeline/steps/gatk.sh
mitopipeline/steps/read_depths.py
mitopipeline/steps/remove_numts_no_split_gap.sh
mitopipeline/steps/removenumts.sh
mitopipeline/steps/snpeff.sh
mitopipeline/steps/split_bams.py
mitopipeline/steps/splitgap.sh
mitopipeline/steps/submit_job.sh
mitopipeline/steps/dbsnp/mtONLY.vcf
mitopipeline/steps/dbsnp/mtONLY.vcf.idx
mitopipeline/steps/tools/AddOrReplaceReadGroups.jar
mitopipeline/steps/tools/FixMateInformation.jar
mitopipeline/steps/tools/MarkDuplicates.jar
mitopipeline/steps/tools/SamToFastq.jar