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* [[vcfCooker]]
* [[vcfCooker]]
* [[thunderVCF]]
* [[thunderVCF]]
== Common Problems ==
If you ran UMAKE without success, please double check these pre-requeists.
Input region file (BED) should only contain chromosome 1, 2, ... 22, X, Y
BAM index files (e.g. bams.index) should use absolute path for each BAM files
Your working partition (where OUTPUT_ROOT specified) should support symbolic link. So Windows partition will not work.
If UMAKE complains about resoures file (e.g. Cannot find HapMap SNPs or 1000 Genome indels), please check your UMAKE configuration file have correct set up resources files in the correct location. A common mistake is to use path HapMap/ while the resource folder is HapMap3/ .
== Acknowledgements ==
== Acknowledgements ==
UMAKE is a result from collaborative effort by Hyun Min Kang, Goo Jun, Carlo Sidore, Yun Li, Paul Anderson, Mary Kate Trost, Wei Chen, Tom Blackwell, and Goncalo Abecasis. Please email to Hyun Min Kang [[mailto:hmkang@umich.edu| hmkang@umich.edu ]] for any questions.
UMAKE is a result from collaborative effort by Hyun Min Kang, Goo Jun, Carlo Sidore, Yun Li, Paul Anderson, Mary Kate Trost, Wei Chen, Tom Blackwell, and Goncalo Abecasis. Please email to Hyun Min Kang [[mailto:hmkang@umich.edu| hmkang@umich.edu ]] for any questions.
