Metadata-Version: 2.1
Name: camu
Version: 0.0.11
Summary: A package for filtering candidate mutations for spontaneous mutation rate estimates.
Home-page: https://gitlab.rlp.net/nruffini/camufi/tree/master
Author: Nicolas Ruffini
Author-email: ruffini@uni-mainz.de
License: UNKNOWN
Description: <p align="center">
          <img height="200" src="images/Camufi_py.png" alt="Camufipy Logo"/>
        </p>
        
        # Filtering false-positive candidate mutations to accelerate DNM-counting for direct µ estimates
        
        For direct estimation of the spontaneous mutation rate µ, it is necessary to calculate the rate of spontaneous de-novo mutations (DNM) occuring per site per generation.
        Consequently, counting DNM is essential for estimating µ.
        
        The raw approach is:
        * Sequencing samples and control --> .fastq files
        * Assembly of sequencing results --> .bam files
        * perform some filtering steps
        * Variant calling 
        * extraction of variants occurring in samples but not in control --> candidate mutations
        
        The resulting list of candidate mutations (CM) currently has to be manually curated using a genome browser like IGV.
        
        Unfortunately, approx. 90 % of these CM are no true DNM, they turn out to be false-positives.
        
        **Camufi.py** aims to accelerate the whole procedure of DNM counting by filtering out the vast majority of false-positive CM and by preparing the remaining CM for fast manual curation with IGV. 
        
        **Camufi.py** consists of 3 main Python modules:
        1. `filterDupAndLinked.py`  
        2. `detectFIO.py`
        3. `snapshotIGV.py`
        
        
        
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: Unix
Description-Content-Type: text/markdown
