#======================================================================
#   GotCloud README
#======================================================================
See http://genome.sph.umich.edu/wiki/GotCloud for full GotCloud documentation.

#----------------------------------------------------------------------
#   Build GotCloud
#----------------------------------------------------------------------
Before running GotCloud, you need to compile the source:
 cd src/; make; cd ..

#----------------------------------------------------------------------
#   Test GotCloud
#----------------------------------------------------------------------
To test the GotCloud aligner, run:

  gotcloud align --test ~/testalign

  This will create/clear the output directory ~/testalign.
  Test results and a log file are put in this directory.
  Results are self-checked and if errors should occur, it will be obvious.


To test the GotCloud umake, run:

  gotcloud snpcall --test ~/testsnp

  This will create/clear the output directory ~/testsnp.
  Test results and a log file are put in this directory.
  Results are self-checked and if errors should occur, it will be obvious.



#----------------------------------------------------------------------
#   General Help for Variant Calling
#----------------------------------------------------------------------

Variant Calling requires three types of input files:
  (1) a set of BAM files
      For high quality SNP calls BAM files should already be:
      * duplicate-marked 
      * base-quality recalibrated
  (2) index file
      Each line contains at least 3 space-separated columns representing a single individual:
      [SAMPLE_ID] [COMMA SEPARATED POPULATION LABELS] [BAM_FILE1] [BAM_FILE2] ...
      1 or more BAMs are allowed per individual
  (3) configuration file
      Contains run-time options & command line arguments.  
      A default configuration is provided.
      User must specify:
      * BAM_INDEX =   # the path/name of the index file
      * OUT_DIR

      Optional specifications...
      * CHRS = #space separated list of chromosomes - defaults to 1-22 & X

      Refer to the default configuration & the wiki page for more information on other settings.
         * http://genome.sph.umich.edu/wiki/GotCloud:_Variant_Calling_Pipeline#Configuration_File

Optional input files:
   * Pedigree files (PED format) (to specify gender information in chrX calling)
   * Target information (UCSC's BED format) in targeted or whole exome capture sequencing

Once these files are configured, to run snp calling and process the data:
   {path}gotcloud snpcall --conf {conf_file} \
      --outdir {output_directory} --numjobs {# of threads to use for processing}