A tool to get maximum likely accession in database
Project description
# 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.
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