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Revision as of 17:09, 17 December 2014
, 17:09, 17 December 2014→Normalization
== Setup in person at the SeqShop Workshop ==
== Setup in person at the SeqShop Workshop ==
''This section is specifically for the SeqShop Workshop computers.''
''This section is specifically for the SeqShop Workshop computers.''
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''If you are not running during the SeqShop Workshop, please skip this section.''
''If you are not running during the SeqShop Workshop, please skip this section.''
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== Setup when running on your own outside of the SeqShop Workshop ==
== Setup when running on your own outside of the SeqShop Workshop ==
''This section is specifically for running on your own outside of the SeqShop Workshop.''
''This section is specifically for running on your own outside of the SeqShop Workshop.''
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''If you are running during the SeqShop Workshop, please skip this section.''
''If you are running during the SeqShop Workshop, please skip this section.''
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It is usually useful to examine the call sets against known data sets for the passed variants.
It is usually useful to examine the call sets against known data sets for the passed variants.
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''Command to use at SeqShop Workshop:''
''Command to use at SeqShop Workshop:''
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''Commands outside of SeqShop Workshop:''
''Commands outside of SeqShop Workshop:''
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We perform the same analysis for the failed variants again, the relatively low overlap with known data sets imply a reasonable tradeoff in sensitivity and specificity.
We perform the same analysis for the failed variants again, the relatively low overlap with known data sets imply a reasonable tradeoff in sensitivity and specificity.
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''Command to use at SeqShop Workshop:''
''Command to use at SeqShop Workshop:''
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''Command outside of SeqShop Workshop:''
''Command outside of SeqShop Workshop:''
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UMICH's algorithm for normalization has been adopted by Petr Danecek in bcftools and is also used in GKNO.
UMICH's algorithm for normalization has been adopted by Petr Danecek in bcftools and is also used in GKNO.
== Return to Workshop Wiki Page ==
Return to main workshop wiki page: [[SeqShop: December 2014]]
