PonyTools

Tools for analyzing Variant (VCF) data and the MNEc Affymetrix SNP Chip

Inlcudes python classes for:

• VCFs
• Axiom Genotype Calls
• FASTA files
• VCF style variants

Includes command line tools to:

• Convert AxiomCalls to VCFs
• Conform VCFs for genotype imputation
• Calculate Concordance between VCF Files
• Calculate Precision and Recall using different scores between a test VCF and a reference VCF
• Plot various summary statistics from VCF files
• Calculate the Di statistic using VCF files

Installation

Ponytool was developed using python 3.6

For best results, install ponytools into a fresh virtual environment.

# using anaconda virtual env
conda create -n ponytools_env python=3
source activate ponytools_env

Stable Version

The most recent recent stable version is on pypi

pip install ponytools

Bleeding Edge version

To install the developmental version from github:

pip install -e git+https://github.com/schae234/PonyTools.git#egg=ponytools

Check that installation worked

$ ponytools --help

usage: ponytools [-h] [--debug] [--interactive] [--overlook] [--version]
                 Available Commands ...

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optional arguments:
  -h, --help          show this help message and exit
  --debug             Drop into ipdb when something bad happens.
  --interactive       Initiate an ipdb session right before exiting.
  --overlook          Skip analysis if files produced by --out exists.
  --version           Print version information and exit.

Ponytools. Tools related to analyzing the MNEc SNP Chip:
  Use --help with each command for more info

  Available Commands
    help              Prints this help message
    Axiom2VCF (a2vcf)
                      Convert Axiom calls to a VCF file.
    conformVCF        Conform a VCF based on a FASTA File and MNEc2M
                      Annotations
    sortVCF           Sort a VCF file based on a FASTA file
    compareVCF        compare two VCFs. No need to be sorted or conformed, we
                      will handle that!
    VCFInfo           Print information about a VCF File
    VCFStats          Plot stats/histograms based on VCF values, e.g. alt-
                      freq, call_rate, etc.
    VCFPR             Compare precision vs recall of two VCFs
    Di                Python implementation of DI script
    samples           List and Manipulate Samples
    imputation        Setup the imputation pipeline
    dosageR2          Calculate the Dosage r^2 between reference and imputed
                      SNPs

"You aren't even on the right chromosome!"