https://github.com/cbrueffer/misc_bioinf

Repository for miscellaneous bioinformatics scripts that may be useful to others.
https://github.com/cbrueffer/misc_bioinf

bioinformatics liftover variant-annotations

Last synced: 24 days ago
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Repository for miscellaneous bioinformatics scripts that may be useful to others.

• Host: GitHub
• URL: https://github.com/cbrueffer/misc_bioinf
• Owner: cbrueffer
• License: bsd-2-clause
• Created: 2013-04-04T09:09:38.000Z (over 11 years ago)
• Default Branch: master
• Last Pushed: 2017-02-07T14:23:00.000Z (over 7 years ago)
• Last Synced: 2023-04-01T10:22:44.235Z (over 1 year ago)
• Topics: bioinformatics, liftover, variant-annotations
• Language: Python
• Homepage:
• Size: 20.5 KB
• Stars: 2
• Watchers: 3
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE.md

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README

        
misc_bioinf

===========

Repository for miscellaneous bioinformatics scripts that may be useful to others.

maf2annovar.py

--------------

Converts a file in MAF format (e.g., from TCGA mutation calling) into the [Annovar](http://annovar.openbioinformatics.org) input format.

Compatible with Python 2 and 3; no external dependencies.

```

usage: maf2annovar.py [-h] [-d] -m MAF_FILE [-v]

Convert a MAF file to Annovar input format.

optional arguments:

  -h, --help            show this help message and exit

  -d, --debug           Enable debug output

  -m MAF_FILE, --maf_file MAF_FILE

                        File in MAF format

  -v, --version         show program's version number and exit

```

liftover_annovar.py

-------------------

Converts the genomic coordinates in an Annovar input file over to a new reference genome using the [UCSC liftOver](https://genome.ucsc.edu/cgi-bin/hgLiftOver) commandline tool.

Compatible with Python 2 and 3; depends on the [pandas](http://pandas.pydata.org/) library.

This script requires a liftOver file in [chain format](https://genome.ucsc.edu/goldenpath/help/chain.html) that maps coordinates between the old and new reference genome.  Chain files for many genomes are available from [UCSC](http://hgdownload.cse.ucsc.edu/downloads.html).

```

usage: liftover_annovar.py [-h] [-d] [-v] -c CHAINFILE -i INFILE [-l LIFTOVER]

                           [-w WORKDIR]

Lift over a file in Annovar format to a new reference genome. Extra columns are

preserved.

optional arguments:

  -h, --help            show this help message and exit

  -d, --debug           enable debug mode

  -v, --version         show program's version number and exit

  -c CHAINFILE, --chainfile CHAINFILE

                        liftOver chain file (available from UCSC)

  -i INFILE, --infile INFILE

                        file in Annovar input format (chromosome, start, end,

                        ref_allele, var_allele, ...)

  -l LIFTOVER, --liftover LIFTOVER

                        path to the liftOver binary (default: system PATH)

  -w WORKDIR, --workdir WORKDIR

                        work directory (default: directory containing INFILE)

```

fix_tophat_unmapped_reads.py

----------------------------

This script has been renamed to ```tophat-recondition ``` and moved to its own repository here: [https://github.com/cbrueffer/tophat-recondition](https://github.com/cbrueffer/tophat-recondition)