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, 17:56, 3 October 2013
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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> |
− | ** <code>path/</code> contains <code>dbsnp_135_b37.rod.chr20.map</code> for each chromosome being processed
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| * 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> |
− | ** <code>path/</code> contains <code>hapmap3.qc.poly.chr20.bim</code> & <code>hapmap3.qc.poly.chr20.frq</code> for each chromosome being processed
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− | A set of reference files can be downloaded from: [[ftp://share.sph.umich.edu/1000genomes/umake-resources/ | FTP Download of Full Resource Files]]
| + | 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. |
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| Configuration File Example Reference Settings: | | Configuration File Example Reference Settings: |