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94 bytes added
, 09:41, 4 April 2013
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| ** Configuration File Setting: <code>INDEL_PREFIX = path/indels.sites.hg19</code> | | ** Configuration File Setting: <code>INDEL_PREFIX = path/indels.sites.hg19</code> |
| ** <code>path/</code> contains <code>indels.sites.hg19.chr20.vcf</code> for each chromosome being processed | | ** <code>path/</code> contains <code>indels.sites.hg19.chr20.vcf</code> for each chromosome being processed |
− | * DBSNP File Prefix | + | * DBSNP File vcf.gz file (must be indexed with tabix) |
− | ** Configuration File Setting: <code>DBSNP_PREFIX = path/dbsnp_135_b37.rod</code> | + | ** Configuration File Setting: <code>DBSNP_PREFIX = path/dbsnp_135.b37.vcf.gz</code> |
| ** <code>path/</code> contains <code>dbsnp_135_b37.rod.chr20.map</code> for each chromosome being processed | | ** <code>path/</code> contains <code>dbsnp_135_b37.rod.chr20.map</code> for each chromosome being processed |
− | * HapMap3 polymorphic site prefix | + | * HapMap3 polymorphic site vcf.gz file (must be indexed with tabix) |
− | ** Configuration File Setting: <code>HM3_PREFIX = path/hapmap3.qc.poly</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 | | ** <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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| REF = path/file.fa | | REF = path/file.fa |
| INDEL_PREFIX = path/indels.sites.hg19 | | INDEL_PREFIX = path/indels.sites.hg19 |
− | DBSNP_PREFIX = path/dbsnp_135_b37.rod | + | DBSNP_PREFIX = path/dbsnp_135_b37.vcf.gz |
− | HM3_PREFIX = path/hapmap3.qc.poly | + | HM3_PREFIX = path/hapmap_3.3.b37.sites.vcf.gz |
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| == Configuration File == | | == Configuration File == |