Metadata-Version: 2.0
Name: SNPmatch
Version: 1.2.2
Summary: A tool to get maximum likely accession in database
Home-page: https://github.com/Gregor-Mendel-Institute/snpmatch
Author: ['Rahul Pisupati']
Author-email: rahul.bharadwaj.p@gmail.com
License: GMI
Keywords: Genotyping Low Coverage sequencing data
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Developers
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Programming Language :: Python :: 3.4
Requires-Dist: scipy (>=0.17.0)
Requires-Dist: numpy (>=1.6.1)
Requires-Dist: PyGWAS
Requires-Dist: vcfnp
Requires-Dist: pandas

# snpmatch

snpmatch is a simple library to compare the given SNPs to that of database SNP matrix and identify the right accession. It is used ot genotype a sample from the low-coverage sequencing data. 
It calculates a likelihood score with a each accession and performs a likelihood ratio test of top accession with rest. 

Requirements:
The snpmatch uses various python packages (numpy, pandas, pygwas, vcfnp)
The main SNP database should be a HDF5 file with specific keys. Mainly read using pygwas package. 





