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A script to parse and verify migrate-n infiles with loads

Project description

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INTRODUCTION

In our experience, Migrate-N does not work well with monomorphic loci. migverify will go through your infile, and output an infile_clean.

By default, migverify will remove all loci that have fewer than two haplotypes, and will remove loci with samples with more than 10% missing data. These values can be changed.

INSTALLATION

migverify is written in Python3 (requires version >=3.6). It can be installed with pip:

`pip3 install migverify`

To get the latest version:

`pip3 install git+https://www.github.com/andersgs/migverify.git`

USAGE

Installation will make available a script called run_migverify, which should be in your PATH.

You can checkout the help with:

`run_migverify --help`

Running with default settings

`run_migverify infile`

Filter out loci with fewer than 3 haplotypes

`run_migverify -m 3 infile`

Filter out loci with samples with more than 20% missing data

`run_migverify -p 0.2 infile`

QUESTIONS or ISSUES

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