Changes

== Example Configuration File ==

== Example Configuration File ==

Example configuration file where reference files are stored in /path/reference, and bam index file in path/freeze5

Example configuration file where reference files happen to be stored in /path/reference, and bam index file in path/freeze5

  CHRS = 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22

  CHRS = 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22

  BAM_INDEX = /path/freeze5/freeze5.bam.index  ### The BAM index file described above

  BAM_INDEX = /path/freeze5/freeze5.bam.index  ### The BAM index file described above

  REF = /path/reference/hs37d5.fa              ### Reference sequence

  REF = /path/reference/hs37d5.fa              ### Reference sequence

  INDEL_PREFIX = /path/reference/1kg.pilot_release.merged.indels.sites.hg19  ### Known indel sites

  INDEL_PREFIX = /path/reference/1kg.pilot_release.merged.indels.sites.hg19  ### Known indel sites

  HM3_PREFIX = /path/reference/hapmap3_r3_b37_fwd.consensus.qc.poly          ### HapMap variants

  HM3_VCF = /path/reference/hapmap3_r3_b37.sites.vcf.gz    ### HapMap variants (requires tabix index file in same directory)

  DBSNP_PREFIX = /path/reference/dbsnp_129_b37.rod                            ### dbSNP variants

  DBSNP_VCF = /path/reference/dbsnp_135.b37.sites.vcf.gz  ### dbSNP variants (requires tabix index file in same directory)

= Running =

= Running =