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        "author": "Allison Seiden",
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        "description": "===========\nSorting Hat\n===========\n\nSorts indels into classes defined as follows:\n  - **homopolymer run (HR):** mutation is in a region where there are 6 or more\n    copies of the nucleotide being inserted or deleted\n  - **change in copy count (CCC):** the allele being inserted or deleted has 1 or\n    more repeats in the mutation region\n  - **no change in copy count (non-CCC):** the allele being inserted or deleted is\n    not repeated in the mutation region\n\nIn order to use sorting_hat, you must ensure the following are installed:\n  - `Python >=3.5.0`_\n  - `bedtools >=2.27.0`_\n\n\nTo install, use *pip*:\n\n.. code-block::\n\n    pip install sorting_hat\n\n\nExample run\n\n.. code-block:: bash\n\n    sorting_hat --bed test.bed \\\n                --fasta test.fasta \\\n                --repeat repeat_masker.txt\n\nUsage\n\n.. code-block::\n\n    sorting_hat [-h] -b BED -f FASTA -r REPEAT [-o OUTPUT]\n\nSorts indels into mutational classes\n\n  -b BED, --bed BED     Location of BED file with all variants. Must be\n                        formatted as Chrom/Start/End/Ref/Alt/PatientID.\n  -f FASTA, --fasta FASTA\n                        Location of reference fasta file.\n  -r REPEAT, --repeat REPEAT\n                        Location of RepeatMasker file downloaded from UCSC\n                        Genome Browser. Refer to docs to see how to download\n                        RepeatMasker.\n  -o OUTPUT, --output OUTPUT\n                        Name of output file, if not chosen then will print to\n                        stdout.\n\nTo download RepeatMasker from UCSC Genome Browser, see photos in 'data'\nfolder on github: https://github.com/allisonseiden/sorting_hat\n\nAllison Seiden <ahseiden@gmail.com>\n\n\n.. _Python >=3.5.0: https://www.python.org/downloads/release/python-350/\n.. _bedtools >=2.27.0: http://bedtools.readthedocs.io/en/latest/\n\n\n",
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