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GotCloud: Variant Calling Pipeline (view source)

Revision as of 14:04, 6 November 2012

121 bytes added ,  14:04, 6 November 2012
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Reference files are required for doing Variant Calling.   
 
Reference files are required for doing Variant Calling.   
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See [[#Reference Files| Configuration Files: Reference Files]] for information on how to specify the reference files in the configuration.
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* Reference Sequence in fasta format.
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** Configuration File Setting:  <code>REF = path/file.fa</code>
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* Indel VCF File Prefix
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** Configuration File Setting:  <code>INDEL_PREFIX = path/indels.sites.hg19</code>
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** <code>path/</code> contains <code>indels.sites.hg19.chr20.vcf</code> for each chromosome being processed
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* DBSNP File Prefix
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** Configuration File Setting:  <code>DBSNP_PREFIX = path/dbsnp_135_b37.rod</code>
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** <code>path/</code> contains <code>dbsnp_135_b37.rod.chr20.map</code> for each chromosome being processed
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* HapMap3 polymorphic site prefix
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** Configuration File Setting:  <code>HM3_PREFIX = path/hapmap3.qc.poly</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
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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]]
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Configuration File Example Reference Settings:
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REF = path/file.fa
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INDEL_PREFIX = path/indels.sites.hg19
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DBSNP_PREFIX = path/dbsnp_135_b37.rod
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HM3_PREFIX = path/hapmap3.qc.poly
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==== Reference Files ====
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==== Configure Reference Files ====
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* Reference Sequence in fasta format.
+
See [[#Reference Files| Reference Files]] for information on how to specify the reference files.
−
** REF = path/file.fa
  −
* Indel VCF File Prefix
  −
** INDEL_PREFIX = path/indels.sites.hg19
  −
** path/ contains indels.sites.hg19.chr20.vcf for each chromosome being processed
  −
* DBSNP File Prefix
  −
** DBSNP_PREFIX = path/dbsnp_135_b37.rod
  −
** path/ contains dbsnp_135_b37.rod.chr20.map for each chromosome being processed
  −
* HapMap3 polymorphic site prefix
  −
** HM3_PREFIX = path/hapmap3.qc.poly
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** path/ contains hapmap3.qc.poly.chr20.bim & hapmap3.qc.poly.chr20.frq for each chromosome being processed
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Can be downloaded from: [[ftp://share.sph.umich.edu/1000genomes/umake-resources/ | FTP Download of Full Resource Files]]
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INDEL_PREFIX = $(UMAKE_ROOT)/ref/indels/1kg.pilot_release.merged.indels.sites.hg19 # 1000 Genomes Pilot 1 indel VCF prefix
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DBSNP_PREFIX =  $(UMAKE_ROOT)/ref/dbSNP/dbsnp_135_b37.rod # dbSNP file prefix
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HM3_PREFIX =  $(UMAKE_ROOT)/ref/HapMap3/hapmap3_r3_b37_fwd.consensus.qc.poly # HapMap3 polymorphic site prefix
      
==== Chromosome X Calling ====
 
==== Chromosome X Calling ====
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/5741"

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