Changes

=== Example Configuration File ===

=== Example Configuration File ===

Example configuration file where reference files happen to be 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 = 20 22

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

  BAM_LIST = /path/freeze5.bam.list

  OUT_DIR = /path/freeze5/output              ### Directory in which to put all gotcloud output

  OUT_DIR = /path/freeze5/output

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

  REF_DIR = /path/reference/

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

REF = $(REF_DIR)/hs37d5.fa

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

  INDEL_PREFIX = $(REF_DIR)/1kg.pilot_release.merged.indels.sites.hg19

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

  HM3_VCF = $(REF_DIR)/hapmap3_r3_b37.sites.vcf.gz

  DBSNP_VCF = $(REF_DIR)/dbsnp_135.b37.sites.vcf.gz

== Running ==

== Running ==