Nescent ngs 2011:Notebook/nescent ngs 2011

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* [http://sourceforge.net/apps/mediawiki/samtools/index.php?title=SAM_protocol Here]'s a nice overview of a basic alignment and variant calling workflow based on SAMtools and GATK
* [http://sourceforge.net/apps/mediawiki/samtools/index.php?title=SAM_protocol Here]'s a nice overview of a basic alignment and variant calling workflow based on SAMtools and GATK
* A more in-depth variant detection [http://www.broadinstitute.org/gsa/wiki/index.php/Best_Practice_Variant_Detection_with_the_GATK_v3 strategy] based on GATK
* A more in-depth variant detection [http://www.broadinstitute.org/gsa/wiki/index.php/Best_Practice_Variant_Detection_with_the_GATK_v3 strategy] based on GATK
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* [http://gage.cbcb.umd.edu/index.html GAGE]
==Notes==
==Notes==

Revision as of 17:55, 14 October 2011

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Welcome!

  • Share notes and comments from the course and beyond!
  • Nescent hosted course materials are here
  • Helpful notes and tutorials from the MSU course are here
  • Here's a nice overview of a basic alignment and variant calling workflow based on SAMtools and GATK
  • A more in-depth variant detection strategy based on GATK
  • GAGE

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