MigVerify: Test and clean up Migrate-N infile with many sequence loci.
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`
