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'''ExomePicks''' is a program that suggests individuals to be sequenced in a large pedigree. '''ExomePicks''' assumes that a genotyping chip or another cost effective means will be used to determine IBD sharing in the pedigree and that, subsequently, one would like to sequence a minimal number of individuals and use their sequences together with IBD information to deduce the sequence of other individuals in the pedigree.
[[Category:Software]]
'''ExomePicks''' is a program that suggests individuals to be sequenced in a large pedigree. '''ExomePicks''' assumes that a genotyping chip or another cost effective means will be used to determine IBD sharing in the pedigree and that, subsequently, one would like to sequence a minimal number of individuals and use their sequences together with IBD information to deduce the sequence of other individuals in the pedigree. We are currently using it in the context of whole exome and whole genome sequencing studies to pick individuals to be sequenced from large family collections.
== Download ==
== Download ==
A source code package can be downloaded from [http://www.sph.umich.edu/csg/abecasis/downloads/generic-ExomePicks-2010-04-12.tar.gz here].
A source code package can be downloaded from [http://csg.sph.umich.edu//abecasis/downloads/generic-ExomePicks-2010-04-12.tar.gz here]. A Windows version can be found [http://csg.sph.umich.edu//cfuchsb/ExomePicks_Windows.zip here]
An extended version of the package which produces output for the visualization with ExomePicksViewer is under development; for details contact [mailto:cfuchsb@umich.edu Christian Fuchsberger].
== Input Files ==
== Input Files ==
In this case, sequencing 8 individuals would provide information on 13 genomes.
In this case, sequencing 8 individuals would provide information on 13 genomes.
== Improvements Under Consideration ==
* Change sorting so that the most valuable individuals for each pedigree are picked first. When resources are limited, it might not be affordable to sequence enough individuals to completely impute each pedigree. This scoring order would allow one to more easily focus on the highest value individuals in each pedigree.
* Implement the ability to evaluate only nuclear families, ignoring the possibility of imputing more distant relatives.
* Add the summed number of sequenced or imputed affecteds to the per family output.
* Unrelated single individuals (''founders'' without offspring) are currently scored as zero value. These should more accurately be scored as single genomes.
== Acknowledgements ==
== Acknowledgements ==
John Blangero at the Southwest Foundation for testing initial version.
Weimin Chen and Serena Sanna for discussions that contributed to the initial version of this program. John Blangero at the Southwest Foundation for testing initial version.
