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Tutorial: GotCloud (view source)

Revision as of 01:26, 8 January 2013

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==Aligning a Sample==
 
==Aligning a Sample==
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As an example, we can analyze the sample files used in the automatic test.
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As an example, we can align the sample files used in the automatic test.
    
To make this easier, change to the {ROOT_DIR}/test/align directory. (We will call the directory in which GotCloud is installed "{ROOT_DIR}".) It contains an index file and a configuration file that can be used directly.
 
To make this easier, change to the {ROOT_DIR}/test/align directory. (We will call the directory in which GotCloud is installed "{ROOT_DIR}".) It contains an index file and a configuration file that can be used directly.
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  PLINK = $(REF_DIR)/hapmap_3.3.b37.chr20
 
  PLINK = $(REF_DIR)/hapmap_3.3.b37.chr20
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If you are in the test/align directory, you can use this file as-is. If you are using a different index file, make sure your index file is named correctly in the first line.
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If you are in the {ROOT_DIR}/test/align directory, you can use this file as-is. If you are using a different index file, make sure your index file is named correctly in the first line. If you are not running this from {ROOT_DIR}/test/align, make sure your configuration and index files are in the same directory.
    
===Running the alignment pipeline===
 
===Running the alignment pipeline===
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  {ROOT_DIR}/bin/gen_biopipeline.pl --conf test.conf --out_dir {OUT_DIR}
 
  {ROOT_DIR}/bin/gen_biopipeline.pl --conf test.conf --out_dir {OUT_DIR}
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where {OUT_DIR} is the directory in which you wish to store the resulting BAM files.
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where {OUT_DIR} is the directory in which you wish to store the resulting BAM files (for example, ~/out).
    
If everything went well, you will see the following messages:
 
If everything went well, you will see the following messages:
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  Finished creating makefile {OUTDIR}/Makefiles/biopipe_Sample2.Makefile
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  Finished creating makefile {OUT_DIR}/Makefiles/biopipe_Sample2.Makefile
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  Finished creating makefile {OUTDIR}/Makefiles/biopipe_Sample1.Makefile
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  Finished creating makefile {OUT_DIR}/Makefiles/biopipe_Sample1.Makefile
 
  --------------------------------------------------------------------
 
  --------------------------------------------------------------------
 
  Run the following commands:
 
  Run the following commands:
 
   
 
   
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  make -f {OUTDIR}/Makefiles/biopipe_Sample2.Makefile > {OUTDIR}/Makefiles/biopipe_Sample2.Makefile.log
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  make -f {OUT_DIR}/Makefiles/biopipe_Sample2.Makefile > {OUT_DIR}/Makefiles/biopipe_Sample2.Makefile.log
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  make -f {OUTDIR}/Makefiles/biopipe_Sample1.Makefile > {OUTDIR}/Makefiles/biopipe_Sample1.Makefile.log
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  make -f {OUT_DIR}/Makefiles/biopipe_Sample1.Makefile > {OUT_DIR}/Makefiles/biopipe_Sample1.Makefile.log
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where {OUTDIR} will be replaced with the directory you entered above.
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where {OUT_DIR} will be replaced with the directory you entered above.
    
====Running the Makefiles====
 
====Running the Makefiles====
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To run a Makefile, simply enter one-by-one the commands generated in the previous step. The log files for the runs will be found in the Makefiles directory, while the BAM files will be found in the {OUT_DIR}/alignment.recal directory.
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To run a Makefile, simply enter one-by-one the commands generated in the previous step. If you wish to run the alignment in the background, add "&" after the make command, as follows:
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make -f {OUT_DIR}/Makefiles/biopipe_Sample2.Makefile > {OUT_DIR}/Makefiles/biopipe_Sample2.Makefile.log &
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The log files for the runs will be found in the Makefiles directory, while the BAM files will be found in the {OUT_DIR}/alignment.recal directory.
       
==Analyzing a Sample==
 
==Analyzing a Sample==
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Using umake, you can analyze the BAM files generated in the previous step and generate a VCF file.
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Using umake, you can analyze the BAM files generated in the previous step and generate a VCF file.  Once again, we can analyze BAM files used in the automatic test.  You will need three files for this: index, configuration, and bed.
    
===Index file===
 
===Index file===
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First, you need a list of all the BAM files to be analyzed. Conveniently, the a test index file (umake_test.index) already exists in {ROOT_DIR}/test/umake/.  It contains the following information:
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NA12272 ALL    bams/NA12272.mapped.ILLUMINA.bwa.CEU.low_coverage.20101123.chrom20.20000001.20300000.bam
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NA12004 ALL    bams/NA12004.mapped.ILLUMINA.bwa.CEU.low_coverage.20101123.chrom20.20000001.20300000.bam
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...
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NA12874 ALL    bams/NA12874.mapped.LS454.ssaha2.CEU.low_coverage.20101123.chrom20.20000001.20300000.bam
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You can use this file directly if you change your current directory to {ROOT_DIR}/test/umake/.
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Alternately, if you want to copy and use this index file to a different directory, you can create a symbolic link to the bams folder as follows:
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ln -s {ROOT_DIR}/test/umake/bams bams
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===BED file===
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This file contains a single line:
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chr20  20000050        20300000
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You can copy this to the current directory and use it as-is.
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===Configuration file===
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A configuration file (umake_test.conf) already exists in {ROOT_DIR}/test/umake/.  It contains the following information:
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CHRS = 20
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TEST_ROOT = $(UMAKE_ROOT)/test/umake
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BAM_INDEX = $(TEST_ROOT)/umake_test.index
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OUT_PREFIX = umake_test
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REF_ROOT = $(TEST_ROOT)/ref
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#
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REF = $(REF_ROOT)/karma.ref/human.g1k.v37.chr20.fa
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INDEL_PREFIX = $(REF_ROOT)/indels/1kg.pilot_release.merged.indels.sites.hg19
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DBSNP_PREFIX =  $(REF_ROOT)/dbSNP/dbsnp_135_b37.rod
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HM3_PREFIX =  $(REF_ROOT)/HapMap3/hapmap3_r3_b37_fwd.consensus.qc.poly
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#
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RUN_INDEX = TRUE        # create BAM index file
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RUN_PILEUP = TRUE      # create GLF file from BAM
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RUN_GLFMULTIPLES = TRUE # create unfiltered SNP calls
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RUN_VCFPILEUP = TRUE    # create PVCF files using vcfPileup and run infoCollector
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RUN_FILTER = TRUE      # filter SNPs using vcfCooker
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RUN_SPLIT = TRUE        # split SNPs into chunks for genotype refinement
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RUN_BEAGLE = FALSE  # BEAGLE - MUST SET AFTER FINISHING PREVIOUS STEPS
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RUN_SUBSET = FALSE  # SUBSET FOR THUNDER - MAY BE SET WITH BEAGLE STEP TOGETHER
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RUN_THUNDER = FALSE # THUNDER - MUST SET AFTER FINISHING PREVIOUS STEPS
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###############################################################################
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WRITE_TARGET_LOCI = TRUE  # FOR TARGETED SEQUENCING ONLY -- Write loci file when performing pileup
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UNIFORM_TARGET_BED = $(TEST_ROOT)/umake_test.bed # Targeted sequencing : When all individuals has the same target. Otherwise, comment it out
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OFFSET_OFF_TARGET = 50 # Extend target by given # of bases
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MULTIPLE_TARGET_MAP =  # Target per individual : Each line contains [SM_ID] [TARGET_BED]
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TARGET_DIR = target    # Directory to store target information
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SAMTOOLS_VIEW_TARGET_ONLY = TRUE # When performing samtools view, exclude off-target regions (may make command line too long)
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If you are running this from a different directory, you will want to change some of the lines as follows:
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BAM_INDEX = {CURRENT_DIR}/umake_test.index
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UNIFORM_TARGET_BED = {CURRENT_DIR}/umake_test.bed
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where {CURRENT_DIR} is the absolute path to the directory that contains the index and bed files.  You may also want to change the name of the output folder:
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OUT_PREFIX = {output_prefix}
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where {output_prefix} is the name of the folder in which you want the output to be stored.
Amkwong
75

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