Authors.rst
LICENSE.txt
MANIFEST.in
NEWS
README.md
setup.cfg
setup.py
mgatk/.DS_Store
mgatk/__init__.py
mgatk/cli.py
mgatk/devnotes.md
mgatk/mgatkHelp.py
mgatk/__pycache__/__init__.cpython-311.pyc
mgatk/__pycache__/cli.cpython-311.pyc
mgatk/__pycache__/mgatkHelp.cpython-311.pyc
mgatk/bin/.DS_Store
mgatk/bin/picard.jar
mgatk/bin/R/convert_cellbender_output.R
mgatk/bin/R/prepare_cellbender.R
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/python/chunk_barcoded_bam.py
mgatk/bin/python/filterClipBam.py
mgatk/bin/python/find_barcodes.py
mgatk/bin/python/oneSample.py
mgatk/bin/python/split_barcoded_bam.py
mgatk/bin/python/sumstatsBP.py
mgatk/bin/python/sumstatsBP_overlap.py
mgatk/bin/python/sumstatsBPtenx.py
mgatk/bin/python/sumstatsBPtenx_overlap.py
mgatk/bin/python/variant_calling.py
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/__pycache__/clidel.cpython-311.pyc
mgatk/deletioncalling/__pycache__/clifind.cpython-311.pyc
mgatk/deletioncalling/bulk_del/plot_deletion_breaks_bulk.R
mgatk/deletioncalling/singles_del/01_process_cell_reads.py
mgatk/deletioncalling/singles_del/02_heteroplasmy_del_singles.R
mgatk/deletioncalling/singles_del/Snakefile.delSingles