Authors.rst
LICENSE.txt
MANIFEST.in
NEWS
README.md
setup.cfg
setup.py
mgatk/__init__.py
mgatk/cli.py
mgatk/devnotes.md
mgatk/mgatkHelp.py
mgatk/__pycache__/__init__.cpython-312.pyc
mgatk/__pycache__/__init__.cpython-314.pyc
mgatk/__pycache__/cli.cpython-312.pyc
mgatk/__pycache__/mgatkHelp.cpython-312.pyc
mgatk/bin/R/toRDS.R
mgatk/bin/anno/fasta/GRCh37.fasta
mgatk/bin/anno/fasta/GRCh38.fasta
mgatk/bin/anno/fasta/GRCm38.fasta
mgatk/bin/anno/fasta/GRCz10.fasta
mgatk/bin/anno/fasta/NC_012920.fasta
mgatk/bin/anno/fasta/hg19.fasta
mgatk/bin/anno/fasta/hg19_chrM.fasta
mgatk/bin/anno/fasta/hg38.fasta
mgatk/bin/anno/fasta/mm10.fasta
mgatk/bin/anno/fasta/mm9.fasta
mgatk/bin/anno/fasta/rCRS.fasta
mgatk/bin/snake/Snakefile.Gather
mgatk/bin/snake/Snakefile.Scatter
mgatk/bin/snake/Snakefile.tenx
mgatk/deletioncalling/clidel.py
mgatk/deletioncalling/clifind.py
mgatk/deletioncalling/processing.py
mgatk/deletioncalling/__pycache__/clidel.cpython-312.pyc
mgatk/deletioncalling/__pycache__/clifind.cpython-312.pyc
mgatk/deletioncalling/__pycache__/processing.cpython-312.pyc
mgatk/deletioncalling/bulk_del/plot_deletion_breaks_bulk.R
mgatk/deletioncalling/singles_del/02_heteroplasmy_del_singles.R
mgatk/deletioncalling/singles_del/Snakefile.delSingles
mgatk/processing/__init__.py
mgatk/processing/allele_counts.py
mgatk/processing/allele_counts_tenx.py
mgatk/processing/barcodes.py
mgatk/processing/dedup.py
mgatk/processing/filtering.py
mgatk/processing/one_sample.py
mgatk/processing/one_slice_tenx.py
mgatk/processing/variant_calling.py
mgatk/processing/__pycache__/__init__.cpython-312.pyc
mgatk/processing/__pycache__/allele_counts.cpython-312.pyc
mgatk/processing/__pycache__/allele_counts_tenx.cpython-312.pyc
mgatk/processing/__pycache__/barcodes.cpython-312.pyc
mgatk/processing/__pycache__/dedup.cpython-312.pyc
mgatk/processing/__pycache__/filtering.cpython-312.pyc
mgatk/processing/__pycache__/one_sample.cpython-312.pyc
mgatk/processing/__pycache__/one_slice_tenx.cpython-312.pyc
mgatk/processing/__pycache__/variant_calling.cpython-312.pyc