mergescan

Description

This program combines pedin, map, and phenotype files of different
genome scans producing 1 genome scan. The markers and alleles can be
either 1. pooled using allele frequency information or 2. renamed so
that same markers across genome scans are analysed separately but
located at the same genetic location.

Usage

mergescan.py -v version -o outputdir [-p phen.dat] scandirlist
             version             must be 1 or 2
             outputdir           is the name of the output directory
             [-p phen.dat]       is a list of phenotype files (see examples)
             scandirlist         is a whitespace delimited list of scan directories to combine(see examples)

Examples

             mergescan.py -v 1 -o combinedscans -p phen.dat -p phen2.dat allscans/*
                    Here 'allscans/' is a directry which contains only scan directories to be combined. A new
                    directory named 'combinedscans' will be created and the combined scan will be placed there.
                    The scans will be combined so that allele frequency information is used. The old phenotype
                    files with the name 'phen.dat' and 'phen2.dat' which were in scan directories will be
                    updated and placed in 'combinedscans'.

             mergescan.py -v 2 -o combinedscans -p phen.dat scandir1/ scandir2/ scandir3/
                    Here 'scandir1/ scandir2/ scandir3/' are the three scan directories which will be combined.
                    A new directory named 'combinedscans' will be created and the combined scan will be placed
                    there. The scans will be combined so that the same marker in diferent scans is renamed and
                    placed so that there genetic distance is less than .001 of one another so that they can be
                    analysed as seperate markers. The old phenotype files with the name 'phen.dat' which were in
                    the scan directories will be updated and placed in 'combinedscans'.

             mergescan.py -v 1 -o combinedscans allscans/*
                    Here 'allscans/' is a directry which contains only scan directories to be combined. A new
                    directory named 'combinedscans' will be created and the combined scan will be placed there.
                    The scans will be combined so that allele frequency information is used.

Example Input/Output files:

Input files:

Assumptions

1. The pedigre file names have the format 'pedin.Z' where Z is the chromosome number.
2. The map file names have the format 'mapZ.dat' where Z is the chromosome number.
3. '0' denotes a missing allele in the genotype file.
4. The pedigree file should be ordered so that all members of the same family are listed
   successively otherwise the script does not retain the correct family structure.
5. It is assumed that for a given marker, all map files which mention the marker give
   it the same marker distance.

Notes

1. In all cases, half typed genotypes are removed.

Author

Kismat Sood