├── .gitignore ├── LICENSE ├── README.md ├── README.rst ├── config.py ├── databases.py ├── depth_gauge.py ├── detect_union_bin_errors.py ├── examples_package ├── README.txt ├── bams_to_get.txt ├── data │ ├── NA12829.FreeBayes.vcf │ ├── NA12829.VarScan.indels.vcf │ ├── NA12829.VarScan.snps.vcf │ ├── NA12830.FreeBayes.vcf │ ├── NA12830.VarScan.indels.vcf │ ├── NA12830.VarScan.snps.vcf │ ├── NA12842.FreeBayes.vcf │ ├── NA12842.VarScan.indels.vcf │ ├── NA12842.VarScan.snps.vcf │ ├── NA12843.FreeBayes.vcf │ ├── NA12843.VarScan.indels.vcf │ ├── NA12843.VarScan.snps.vcf │ ├── NA12872.FreeBayes.vcf │ ├── NA12872.VarScan.indels.vcf │ ├── NA12872.VarScan.snps.vcf │ ├── NA12873.FreeBayes.vcf │ ├── NA12873.VarScan.indels.vcf │ ├── NA12873.VarScan.snps.vcf │ ├── NA12874.FreeBayes.vcf │ ├── NA12874.VarScan.indels.vcf │ ├── NA12874.VarScan.snps.vcf │ ├── NA12878.FreeBayes.vcf │ ├── NA12878.Samtools.vcf │ ├── NA12878.VarScan.indels.vcf │ ├── NA12878.VarScan.snps.vcf │ ├── NA12889.FreeBayes.vcf │ ├── NA12889.VarScan.indels.vcf │ ├── NA12889.VarScan.snps.vcf │ ├── NA12890.FreeBayes.vcf │ ├── NA12890.VarScan.indels.vcf │ ├── NA12890.VarScan.snps.vcf │ ├── example5.json │ ├── geneset.bed │ ├── hotspots.bed │ └── samples.txt ├── depthgauge_setup.sh ├── example_workflow_1 │ ├── projA │ │ ├── NA12829.VarScan.snps.vcf │ │ ├── NA12830.VarScan.snps.vcf │ │ ├── NA12842.VarScan.snps.vcf │ │ ├── NA12843.VarScan.snps.vcf │ │ ├── NA12872.VarScan.snps.vcf │ │ ├── NA12873.VarScan.snps.vcf │ │ ├── NA12874.VarScan.snps.vcf │ │ ├── NA12878.VarScan.snps.vcf │ │ ├── NA12889.VarScan.snps.vcf │ │ ├── NA12890.VarScan.snps.vcf │ │ └── samples.txt │ └── projB │ │ ├── NA12829 │ │ └── NA12829.VarScan.snps.vcf │ │ ├── NA12830 │ │ └── NA12830.VarScan.snps.vcf │ │ ├── NA12842 │ │ └── NA12842.VarScan.snps.vcf │ │ ├── NA12843 │ │ └── NA12843.VarScan.snps.vcf │ │ ├── NA12872 │ │ └── NA12872.VarScan.snps.vcf │ │ ├── NA12873 │ │ └── NA12873.VarScan.snps.vcf │ │ ├── NA12874 │ │ └── NA12874.VarScan.snps.vcf │ │ ├── NA12878 │ │ └── NA12878.VarScan.snps.vcf │ │ ├── NA12889 │ │ └── NA12889.VarScan.snps.vcf │ │ ├── NA12890 │ │ └── NA12890.VarScan.snps.vcf │ │ └── samples.txt ├── example_workflow_2 │ ├── NA12829 │ │ ├── NA12829.FreeBayes.vcf │ │ ├── NA12829.VarScan.indels.vcf │ │ └── NA12829.VarScan.snps.vcf │ ├── NA12830 │ │ ├── NA12830.FreeBayes.vcf │ │ ├── NA12830.VarScan.indels.vcf │ │ └── NA12830.VarScan.snps.vcf │ ├── NA12842 │ │ ├── NA12842.FreeBayes.vcf │ │ ├── NA12842.VarScan.indels.vcf │ │ └── NA12842.VarScan.snps.vcf │ ├── NA12843 │ │ ├── NA12843.FreeBayes.vcf │ │ ├── NA12843.VarScan.indels.vcf │ │ └── NA12843.VarScan.snps.vcf │ ├── NA12872 │ │ ├── NA12872.FreeBayes.vcf │ │ ├── NA12872.VarScan.indels.vcf │ │ └── NA12872.VarScan.snps.vcf │ ├── NA12873 │ │ ├── NA12873.FreeBayes.vcf │ │ ├── NA12873.VarScan.indels.vcf │ │ └── NA12873.VarScan.snps.vcf │ ├── NA12874 │ │ ├── NA12874.FreeBayes.vcf │ │ ├── NA12874.VarScan.indels.vcf │ │ └── NA12874.VarScan.snps.vcf │ ├── NA12878 │ │ ├── NA12878.FreeBayes.vcf │ │ ├── NA12878.VarScan.indels.vcf │ │ └── NA12878.VarScan.snps.vcf │ ├── NA12889 │ │ ├── NA12889.FreeBayes.vcf │ │ ├── NA12889.VarScan.indels.vcf │ │ └── NA12889.VarScan.snps.vcf │ ├── NA12890 │ │ ├── NA12890.FreeBayes.vcf │ │ ├── NA12890.VarScan.indels.vcf │ │ └── NA12890.VarScan.snps.vcf │ └── samples.txt ├── example_workflow_3 │ ├── NA12878 │ │ ├── FreeBayes.vcf │ │ ├── Samtools.vcf │ │ └── VarScan.snps.vcf │ └── samples.txt ├── files_to_get.txt └── setup.sh ├── genes2bed.sh ├── info.py ├── inputs.py ├── mucor.py ├── mucor_config.py ├── mucorfeature.py ├── mucorfilters.py ├── output.py ├── report.py ├── setup.py └── variant.py /.gitignore: -------------------------------------------------------------------------------- 1 | *.pyc 2 | *.bak 3 | notes.txt 4 | mucor.egg-info/ 5 | dist/ 6 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 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