Ligate Minimac

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A script to ligate together chunks created by minimac:

ligate_minimac.py

Usage instructions (can also run the script without arguments, or with -h):

Usage: ligate_minimac.py -o output_prefix <info files>

This script assumes the following:

  1) You are attempting to merge only minimac chunks from the same chromosome

  2) Dosage files and info files end in .dose (or .dose.gz) and .info (or .info.gz)

      i.e. chr9.1.10000.info.gz and chr9.1.10000.dose.gz

  3) Markers within info files are sorted by genomic position

  4) Minimac chunks are disjoint, that is, their markers do not overlap

You must also have the Unix tools join, cut, gzip/gunzip, tail, sort, and cut.
Additionally, the bash shell must be present on your system; you do not need to
be inside a bash shell to run the script, however.

The script will not work under Windows.

Only testing has been done with Python 2.7. Earlier versions of python should
work, but 2.6+ is probably best.

This script makes heavy use of multiple concurrent processes piped together.
Therefore, you should likely only run 1 job at a time on the same machine.

Example:

  ./ligate_minimac.py -o my_merged_results chr9*info.gz



Options:
  -h, --help         show this help message and exit
  -o OUT, --out=OUT  Output file prefix (files OUT.dose.gz and OUT.info.gz
                     will be created)

Contact welchr@umich.edu for questions/issues.