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GotCloud: Variant Calling Pipeline (view source)

Revision as of 17:56, 3 October 2013

93 bytes removed ,  17:56, 3 October 2013
→‎Reference Files
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* DBSNP File vcf.gz file (must be indexed with tabix)
 
* DBSNP File vcf.gz file (must be indexed with tabix)
 
** Configuration File Setting:  <code>DBSNP_VCF = path/dbsnp_135.b37.vcf.gz</code>
 
** Configuration File Setting:  <code>DBSNP_VCF = path/dbsnp_135.b37.vcf.gz</code>
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** <code>path/</code> contains <code>dbsnp_135_b37.rod.chr20.map</code> for each chromosome being processed
   
* HapMap3 polymorphic site vcf.gz file (must be indexed with tabix)
 
* HapMap3 polymorphic site vcf.gz file (must be indexed with tabix)
 
** Configuration File Setting:  <code>HM3_VCF = path/hapmap_3.3.b37.sites.vcf.gz<code>
 
** Configuration File Setting:  <code>HM3_VCF = path/hapmap_3.3.b37.sites.vcf.gz<code>
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** <code>path/</code> contains <code>hapmap3.qc.poly.chr20.bim</code> & <code>hapmap3.qc.poly.chr20.frq</code> for each chromosome being processed
     −
A set of reference files can be downloaded from: [[ftp://share.sph.umich.edu/1000genomes/umake-resources/ | FTP Download of Full Resource Files]]
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See [[GotCloud: Genetic Reference and Resource Files]] for more information on the reference files.
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See [[GotCloud:_Genetic_Reference_and_Resource_Files#Downloadable Reference and Resource Files| GotCloud Downloadable Reference and Resource Files]] for instructions on downloading a set of reference files.
    
Configuration File Example Reference Settings:
 
Configuration File Example Reference Settings:
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/8799"

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