Changes

** <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 vcf.gz file (must be indexed with tabix)

* DBSNP File vcf.gz file (must be indexed with tabix)

** Configuration File Setting:  <code>DBSNP_PREFIX = 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

** <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)

  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.vcf.gz

  DBSNP_VCF = path/dbsnp_135_b37.vcf.gz

  HM3_PREFIX = path/hapmap_3.3.b37.sites.vcf.gz

  HM3_VCF = path/hapmap_3.3.b37.sites.vcf.gz

== Configuration File ==

== Configuration File ==