Merlin exercise

Copy the files from f:\stacey\2001\merlin :

merlin.ped - pedigree file containing mother, father, and 3 offspring
merlin.dat - QTDT format file specifying what is in the ped file
merlin.map - map file specifying distances between loci
sparse.map - map file specifying distances between loci
sample.ped - anonymous genome scan for a common disease
sample2.ped - anonymous genome scan for a common disease (cut in half)

First look for pedigree errors:

Start GRR (Start menu->Genetics->GRR) and load in sample2.ped
Use all-pairs

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Compute singlepoint ibds and save them to merlin.ibd:

Start a DOS Window
cd into where you copied the files


merlin --single --ibd

For each marker, look at the ibd sharing at each locus among the
offspring (sibs), who are individuals 3, 4, and 5 in the pedigree:

grep "1 3 4" merlin.ibd > sib.ibd

Compute multipoint ibds and haplotypes, saved to merlin.ibd & merlin.chr:

merlin --ibd --error --best

Re-examine (using grep) merlin.ibd to see how multipoint ibd estimates
differ from singlepoint.

Look at merlin.chr to see the estimated haplotypes for the family.

What happens if there is a possible genotype error?

merlin -p double.ped --error --best

Would this error have been detected if we used a sparse map?  Modify
merlin.map to change it to a 10cM map.

copy merlin.map sparse.map   and modify

merlin -p double.ped -m sparse.map --error

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As an exercise to be done before Thursday, 

Copy the Keavney data from f:\stacey\2001\ace

pedstats -p merlin.ped -d merlin.dat

merlin --ibd --error --one

Examine the various output files