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[[Category:Software|UMAKE]]
[[Category:Software|UMAKE]]
'''NOTE: The latest version of UMAKE pipeline is now included in [[GotCloud]] package, and the current documentation is outdated. Please visit [[GotCloud]] page for more details on the UMAKE'''
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<div style="font-size:162%; border:none; margin:0; padding:.1em; color:#000;">'''NOTE: The UMAKE pipeline is now included in [[GotCloud]] package and is no longer maintained as a separate download. Please see [[GotCloud]] instead. The documentation on this page is outdated. Please visit [[GotCloud]] page for more details on the latest version'''</div>
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'''UMAKE''' is a software pipeline to detect SNPs and call their genotypes from a list of BAM files. '''UMAKE''' pipeline has been successfully applied in detecting SNPs from many large-scale next-generation sequencing studies.
'''UMAKE''' is a software pipeline to detect SNPs and call their genotypes from a list of BAM files. '''UMAKE''' pipeline has been successfully applied in detecting SNPs from many large-scale next-generation sequencing studies.
== Download UMAKE ==
== Download UMAKE ==
To get a copy go to the [http://www.sph.umich.edu/csg/kang/umake/download UMAKE Download] download page.
To get a copy go to the [http://csg.sph.umich.edu//kang/umake/download UMAKE Download] download page.
== Build UMAKE ==
== Build UMAKE ==
== Exercise with Example Resources ==
== Exercise with Example Resources ==
Example input files can be downloaded at [http://www.sph.umich.edu/csg/kang/umake/download UMAKE Download]. These example resource files includs sequence alignment files over 60 individuals from the 1000 Genomes project, focusing on 300kb region in chromosome 20. Note that the reference genome FASTA file has also been modified to use chromosome 20 only.
Example input files can be downloaded at [http://csg.sph.umich.edu//kang/umake/download UMAKE Download]. These example resource files includs sequence alignment files over 60 individuals from the 1000 Genomes project, focusing on 300kb region in chromosome 20. Note that the reference genome FASTA file has also been modified to use chromosome 20 only.
Let <code>UMAKE_HOME</code> be the path to the UMAKE package and <code>EXAMPLE_HOME</code> be the path to the example resource files.
Let <code>UMAKE_HOME</code> be the path to the UMAKE package and <code>EXAMPLE_HOME</code> be the path to the example resource files.
