Metadata-Version: 2.1
Name: snprocess
Version: 0.1.6
Summary: A SNP processing package
Home-page: https://github.com/dokastho/snprocess
Author: Thomas Dokas
Author-email: dokastho@umich.edu
License: UNKNOWN
Description: # SNPROCESS
          by Thomas Dokas
          
          <dokastho@umich.edu>
          
          SNProcess is a Single Nucleotide Polymorphism (SNP) Quality Control pipeline, written in python
          the procedure was developed by <INSERT LAB NAME HERE>.
        ## QC1
        Steps for QC:
        1. Check missingness and generate plots
        2. Remove individuals with high missingness
        3. Remove individuals with outlying gender SNP's
        4. Select autosomal SNPs only and filter out SNPs with low minor allele frequency (MAF)
        5. Delete SNPs not in the Hardy-WEinberg equilibrium (HWE)
        6. Heterozygosity and LD Pruning
        
        ## QC2
        This portion of the pipeline compares the user data with data in the 1,000 genome project and produces graphs that show the population stratification based on race & ethnicity
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.6
Description-Content-Type: text/markdown
