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UMAKE (view source)

Revision as of 00:35, 7 July 2011

27,240 bytes added ,  00:35, 7 July 2011
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To build UMAKE, download the UMAKE package from the link above and run the following series of commands.
 
To build UMAKE, download the UMAKE package from the link above and run the following series of commands.
−
  tar xzvf umake.v1.20110705.tar.gz
+
  tar xzvf umake.v1.0.1.20110706.tar.gz
 
  cd umake
 
  cd umake
 
  make
 
  make
Line 58: Line 58:  
* BAM files need to be duplicate-marked and base-quality recalibrated in order to obtain high quality SNP calls.
 
* BAM files need to be duplicate-marked and base-quality recalibrated in order to obtain high quality SNP calls.
 
* Each line of Index file represents each individual under the following format. Note that multiple BAMs per individual may be provided.
 
* Each line of Index file represents each individual under the following format. Note that multiple BAMs per individual may be provided.
−
  [SAMPLE_ID] [COMMA SEPARATED POPULATION LABELS] [BAM_FILE1] [BAM_FILE2] ...
+
  [SAMPLE_ID]   [COMMA SEPARATED POPULATION LABELS] [BAM_FILE1] [BAM_FILE2] ...
 
* Additional input Files including Pedigree files (PED format) (to specify gender information in chrX calling), Target information (UCSC's BED format) in targeted or whole exome capture sequencing may be provided.
 
* Additional input Files including Pedigree files (PED format) (to specify gender information in chrX calling), Target information (UCSC's BED format) in targeted or whole exome capture sequencing may be provided.
 
* Configuration file contains core information of run-time options including the software binaries and command line arguments. Refer to the example configuration file for further information
 
* Configuration file contains core information of run-time options including the software binaries and command line arguments. Refer to the example configuration file for further information
 +
 +
== Configuration File ==
 +
 +
The example configuration file below illustrate how to configure the UMAKE configuration file. Here are a few highlights
 +
* Steps to run could be automatically set using --snpcall, --beagle, --thunder, --extract, or manually set by uncommenting options in STEPS_TO_RUN. Note that the steps to run should be in a consecutive order
 +
* To run on full genome data, the resource file should be download at [[ftp://share.sph.umich.edu/1000genomes/umake-resources/ | FTP Download of Full Resource Files]].
 +
* You need to uncomment the target-related configuration lines in order to run in whole genome data
 +
* FILTER_ARGS needs to be carefully calibrated in order to obtain a good set of filtered set of SNPs
 +
 +
##################################################################
 +
# UMAKE CONFIGURATION FILE
 +
# This configuration file contains run-time configuration of
 +
# UMAKE SNP calling pipeline
 +
###############################################################################
 +
## KEY ELEMENTS TO CONFIGURE : NEED TO MODIFY
 +
###############################################################################
 +
UMAKE_ROOT = FULL_PATH_TO_UMAKE  ## e.g. /home/myid/code/umake
 +
INPUT_ROOT = FULL_PATH_TO_CURRENT_DIR ## e.g. /home/myid/data/umake-examples
 +
OUTPUT_ROOT = FULL_PATH_TO_OUTPUT_DIR ## e.g. /home/myid/data/umake-examples/out
 +
BAM_INDEX = $(INPUT_ROOT)/umake-example.index  # SAMPLE INDEX FILE (See documentation for detailed format)
 +
CHRS = 20              # List of chromosomes to call SNPs. For multiple chromosomes, separate by whitespace
 +
OUT_DIR = $(OUTPUT_ROOT)    # output directory
 +
OUT_PREFIX = umake-example  # prefix of output Makefile $(OUT_PREFIX).Makefile will be generated
 +
#PED_INDEX = $(INPUT_ROOT)/umake-example.ped    # SAMPLE PED FILE (required only for chrX calling)
 +
#
 +
###############################################################################
 +
## STEPS TO RUN : COMMENT OUT TO EXCLUDE CERTAIN STEPS
 +
##  --snpcall, --extract, --beagle, --thunder commands automatically set them
 +
###############################################################################
 +
#RUN_INDEX = TRUE        # create BAM index file
 +
#RUN_PILEUP = TRUE      # create GLF file from BAM
 +
#RUN_GLFMULTIPLES = TRUE # create unfiltered SNP calls
 +
#RUN_VCFPILEUP = TRUE    # create PVCF files using vcfPileup and run infoCollector
 +
#RUN_FILTER = TRUE      # filter SNPs using vcfCooker
 +
#RUN_SPLIT = TRUE        # split SNPs into chunks for genotype refinement
 +
#RUN_BEAGLE = TRUE  # BEAGLE - MUST SET AFTER FINISHING PREVIOUS STEPS
 +
#RUN_SUBSET = TRUE  # SUBSET FOR THUNDER - MAY BE SET WITH BEAGLE STEP TOGETHER
 +
#RUN_THUNDER = TRUE # THUNDER - MUST SET AFTER FINISHING PREVIOUS STEPS
 +
#
 +
###############################################################################
 +
## OPTIONS FOR GLFEXTRACT (GLFMULTIPLES, VCFPILEUP, FILTER MUST BE TURNED OFF)
 +
###############################################################################
 +
#RUN_EXTRACT = TRUE  # Instead of discovering SNPs, extract genotype liklihood in the site of VCF_EXTRACT
 +
#VCF_EXTRACT = # whole-genome (gzipped and tabixed) .vcf.gz file to extract the site information to genotype (such as 1000 Genomes site list)
 +
#
 +
###############################################################################
 +
## OPTIONS FOR EXOME/TARGETED SEQUENCING : COMMENT OUT IF WHOLE GENOME SEQUENCING
 +
###############################################################################
 +
WRITE_TARGET_LOCI = TRUE  # FOR TARGETED SEQUENCING ONLY -- Write loci file when performing pileup
 +
UNIFORM_TARGET_BED = $(INPUT_ROOT)/umake-example.bed # Targeted sequencing : When all individuals has the same target. Otherwise, comment it out
 +
OFFSET_OFF_TARGET = 50 # Extend target by given # of bases
 +
MULTIPLE_TARGET_MAP =  # Target per individual : Each line contains [SM_ID] [TARGET_BED]
 +
TARGET_DIR = target    # Directory to store target information
 +
SAMTOOLS_VIEW_TARGET_ONLY = TRUE # When performing samtools view, exclude off-target regions (may make command line too long)
 +
###############################################################################
 +
## RESOURCE FILES : Download the full resources for full genome calling
 +
###############################################################################
 +
REF = $(INPUT_ROOT)/data/ref/human_g1k_v37_chr20.fa # Reference FASTA sequence. Note that the FASTA file in the example package is only chr20.
 +
INDEL_PREFIX = $(INPUT_ROOT)/data/indels/1kg.pilot_release.merged.indels.sites.hg19 # 1000 Genomes Pilot 1 indel VCF prefix
 +
DBSNP_PREFIX =  $(INPUT_ROOT)/data/dbsnp/dbsnp_129_b37.rod # dbSNP file prefix
 +
HM3_PREFIX =  $(INPUT_ROOT)/data/HapMap/hapmap3_r3_b37_fwd.consensus.qc.poly # HapMap3 polymorphic site prefix
 +
###############################################################################
 +
## BINARIES
 +
###############################################################################
 +
SAMTOOLS_FOR_PILEUP = $(UMAKE_ROOT)/bin/samtools-hybrid # for samtools pileup
 +
SAMTOOLS_FOR_OTHERS = $(UMAKE_ROOT)/bin/samtools-hybrid # for samtools view and calmd
 +
GLFMERGE = $(UMAKE_ROOT)/bin/glfMerge # glfMerge when multiple BAMs exist per indvidual
 +
GLFMULTIPLES = $(UMAKE_ROOT)/bin/glfMultiples --minMapQuality 0 --minDepth 1 --maxDepth 10000000 --uniformTsTv --smartFilter # glfMultiples and options
 +
GLFEXTRACT = $(UMAKE_ROOT)/bin/glfExtract  # glfExtract for obtaining VCF for known sites
 +
VCFPILEUP = $(UMAKE_ROOT)/bin/vcfPileup    # vcfPileup to generate rich per-site information
 +
INFOCOLLECTOR = $(UMAKE_ROOT)/bin/infoCollector # create filtering statistics
 +
VCFMERGE = perl $(UMAKE_ROOT)/scripts/bams2vcfMerge.pl # merge multiple BAMs separated by chunk of genomes
 +
VCFCOOKER = $(UMAKE_ROOT)/bin/vcfCooker  # vcfCooker for filtering
 +
VCFSUMMARY = perl $(UMAKE_ROOT)/scripts/vcfSummary.pl # Get summary statistics of discovered site
 +
VCFSPLIT = perl $(UMAKE_ROOT)/scripts/vcfSplit.pl # split VCF into overlapping chunks for genotype refinement
 +
VCFPASTE = perl $(UMAKE_ROOT)/scripts/vcfPaste.pl # vcfPaste to generate filtered genotype VCF
 +
BEAGLE = java -Xmx4g -jar $(UMAKE_ROOT)/ext/beagle.20101226.jar seed=993478 gprobs=true niterations=50 lowmem=true # BEAGLE BINARY : NEED TO COPY BEAGLE TO $(UMAKE_ROOT)/ext DIRECTORY BEFORE RUNNING PIPELINE
 +
VCF2BEAGLE = perl $(UMAKE_ROOT)/scripts/vcf2Beagle.pl --PL # convert VCF (with PL tag) into beagle input
 +
BEAGLE2VCF = perl $(UMAKE_ROOT)/scripts/beagle2Vcf.pl # convert beagle output to VCF
 +
THUNDER = $(UMAKE_ROOT)/bin/thunderVCF -r 30 --phase --dosage --compact --inputPhased # MaCH/Thunder genotype refinement step
 +
LIGATEVCF = perl $(UMAKE_ROOT)/scripts/ligateVcf.pl # ligate multiple phased VCFs while resolving the phase between VCFs
 +
BGZIP = $(UMAKE_ROOT)/ext/bgzip  # NEED TO COPY BGZIP TO $(UMAKE_ROOT)/ext DIRECTORY BEFORE RUNNING PIPELINE
 +
TABIX = $(UMAKE_ROOT)/ext/tabix  # NEED TO COPY TABIX TO $(UMAKE_ROOT)/ext DIRECTORY BEFORE RUNNING PIPELINE
 +
###############################################################################
 +
## ARGUMENT FOR FILTERING
 +
###############################################################################
 +
SAMTOOLS_VIEW_FILTER = -q 20 -F 0x0704 # samtools view filter (-q by MQ, -F by flag)
 +
FILTER_MAX_SAMPLE_DP = 20  # Max Depth per Sample (20x default) -- will generate FILTER_MAX_TOTAL_DP automatically
 +
FILTER_MIN_SAMPLE_DP = 0.5 # Min Depth per Sample (0.5x defaul) -- will generate FILTER_MIN_TOTAL_DP automatically
 +
FILTER_ARGS = --write-vcf --filter --maxDP $(FILTER_MAX_TOTAL_DP) --minDP $(FILTER_MIN_TOTAL_DP) --maxAB 70 --maxSTR 20 --minSTR -20 --winIndel 5 --maxSTZ 5 --minSTZ -5 --maxAOI 5 # arguments for filtering (refer to vcfCooker for details)
 +
#############################################################################
 +
## RELATIVE DIRECTORY UNDER OUT_DIR
 +
#############################################################################
 +
BAM_GLF_DIR = glfs/bams  # BAM level GLF
 +
SM_GLF_DIR = glfs/samples # sample level GLF (after glfMerge if necessary)
 +
VCF_DIR = vcfs            # unfiltered and filtered VCF
 +
PVCF_DIR = pvcfs          # vcfPileup results
 +
SPLIT_DIR = split        # chunks split to multiple overlappingpieces
 +
BEAGLE_DIR = beagle      # beagle output
 +
THUNDER_DIR = thunder    # MaCH/thunder output
 +
GLF_INDEX = glfIndex.ped  # glfMultiples/glfExtract index file info
 +
#############################################################################
 +
## OTHER OPTIONS
 +
#############################################################################
 +
UNIT_CHUNK = 5000000      # Chunk size of SNP calling : 5Mb is default
 +
LD_NSNPS = 10000          # Chunk size of genotype refinement : 10,000 SNPs
 +
LD_OVERLAP = 1000        # Overlapping # of SNPs between chinks : 1,000 SNPs
 +
RUN_INDEX_FORCE = FALSE  # Regenerate BAM index file even if it exists
 +
MERGE_BEFORE_FILTER = FALSE # Merge across the chromosome before filtering
 +
NOBAQ_SUBSTRINGS = SOLID  # Avoid BAQ if the BAM file contains the substring
 +
ASSERT_BAM_EXIST = FALSE  # Check if BAM file exists
 +
#############################################################################
 +
## CLUSTER SETTING : CURRENTLY COMPATIBLE WITH MOSIX PLATFORM
 +
#############################################################################
 +
MOS_PREFIX =    # PREFIX FOR MOSIX COMMAND (BLANK IF UNUSED)
 +
MOS_NODES =      # COMMA-SEPARATED LIST OF NODES TO SUBMIT JOBS
 +
REMOTE_PREFIX =  # REMOTE_PREFIX : Set if cluster node see the directory differently (e.g. /net/mymachine/[original-dir]
 +
host8-223:umake-examples hmkang$ cat umake-example.conf | perl -lne 'chomp; print " $_"'
 +
##################################################################
 +
# UMAKE CONFIGURATION FILE
 +
# This configuration file contains run-time configuration of
 +
# UMAKE SNP calling pipeline
 +
###############################################################################
 +
## KEY ELEMENTS TO CONFIGURE : NEED TO MODIFY
 +
###############################################################################
 +
#UMAKE_ROOT = FULL_PATH_TO_UMAKE  ## e.g. /home/myid/code/umake
 +
#INPUT_ROOT = FULL_PATH_TO_CURRENT_DIR ## e.g. /home/myid/data/umake-examples
 +
#OUTPUT_ROOT = FULL_PATH_TO_OUTPUT_DIR ## e.g. /home/myid/data/umake-examples/out
 +
BAM_INDEX = $(INPUT_ROOT)/umake-example.index  # SAMPLE INDEX FILE (See documentation for detailed format)
 +
CHRS = 20              # List of chromosomes to call SNPs. For multiple chromosomes, separate by whitespace
 +
OUT_DIR = $(OUTPUT_ROOT)    # output directory
 +
OUT_PREFIX = umake-example  # prefix of output Makefile $(OUT_PREFIX).Makefile will be generated
 +
#PED_INDEX = $(INPUT_ROOT)/umake-example.ped    # SAMPLE PED FILE (required only for chrX calling)
 +
#
 +
###############################################################################
 +
## STEPS TO RUN : COMMENT OUT TO EXCLUDE CERTAIN STEPS
 +
##  --snpcall, --extract, --beagle, --thunder commands automatically set them
 +
###############################################################################
 +
#RUN_INDEX = TRUE        # create BAM index file
 +
#RUN_PILEUP = TRUE      # create GLF file from BAM
 +
#RUN_GLFMULTIPLES = TRUE # create unfiltered SNP calls
 +
#RUN_VCFPILEUP = TRUE    # create PVCF files using vcfPileup and run infoCollector
 +
#RUN_FILTER = TRUE      # filter SNPs using vcfCooker
 +
#RUN_SPLIT = TRUE        # split SNPs into chunks for genotype refinement
 +
#RUN_BEAGLE = TRUE  # BEAGLE - MUST SET AFTER FINISHING PREVIOUS STEPS
 +
#RUN_SUBSET = TRUE  # SUBSET FOR THUNDER - MAY BE SET WITH BEAGLE STEP TOGETHER
 +
#RUN_THUNDER = TRUE # THUNDER - MUST SET AFTER FINISHING PREVIOUS STEPS
 +
#
 +
###############################################################################
 +
## OPTIONS FOR GLFEXTRACT (GLFMULTIPLES, VCFPILEUP, FILTER MUST BE TURNED OFF)
 +
###############################################################################
 +
#RUN_EXTRACT = TRUE  # Instead of discovering SNPs, extract genotype liklihood in the site of VCF_EXTRACT
 +
#VCF_EXTRACT = # whole-genome (gzipped and tabixed) .vcf.gz file to extract the site information to genotype (such as 1000 Genomes site list)
 +
#
 +
###############################################################################
 +
## OPTIONS FOR EXOME/TARGETED SEQUENCING : COMMENT OUT IF WHOLE GENOME SEQUENCING
 +
###############################################################################
 +
WRITE_TARGET_LOCI = TRUE  # FOR TARGETED SEQUENCING ONLY -- Write loci file when performing pileup
 +
UNIFORM_TARGET_BED = $(INPUT_ROOT)/umake-example.bed # Targeted sequencing : When all individuals has the same target. Otherwise, comment it out
 +
OFFSET_OFF_TARGET = 50 # Extend target by given # of bases
 +
MULTIPLE_TARGET_MAP =  # Target per individual : Each line contains [SM_ID] [TARGET_BED]
 +
TARGET_DIR = target    # Directory to store target information
 +
SAMTOOLS_VIEW_TARGET_ONLY = TRUE # When performing samtools view, exclude off-target regions (may make command line too long)
 +
###############################################################################
 +
## RESOURCE FILES : Download the full resources for full genome calling
 +
###############################################################################
 +
REF = $(INPUT_ROOT)/data/ref/human_g1k_v37_chr20.fa # Reference FASTA sequence. Note that the FASTA file in the example package is only chr20.
 +
INDEL_PREFIX = $(INPUT_ROOT)/data/indels/1kg.pilot_release.merged.indels.sites.hg19 # 1000 Genomes Pilot 1 indel VCF prefix
 +
DBSNP_PREFIX =  $(INPUT_ROOT)/data/dbsnp/dbsnp_129_b37.rod # dbSNP file prefix
 +
HM3_PREFIX =  $(INPUT_ROOT)/data/HapMap/hapmap3_r3_b37_fwd.consensus.qc.poly # HapMap3 polymorphic site prefix
 +
###############################################################################
 +
## BINARIES
 +
###############################################################################
 +
SAMTOOLS_FOR_PILEUP = $(UMAKE_ROOT)/bin/samtools-hybrid # for samtools pileup
 +
SAMTOOLS_FOR_OTHERS = $(UMAKE_ROOT)/bin/samtools-hybrid # for samtools view and calmd
 +
GLFMERGE = $(UMAKE_ROOT)/bin/glfMerge # glfMerge when multiple BAMs exist per indvidual
 +
GLFMULTIPLES = $(UMAKE_ROOT)/bin/glfMultiples --minMapQuality 0 --minDepth 1 --maxDepth 10000000 --uniformTsTv --smartFilter # glfMultiples and options
 +
GLFEXTRACT = $(UMAKE_ROOT)/bin/glfExtract  # glfExtract for obtaining VCF for known sites
 +
VCFPILEUP = $(UMAKE_ROOT)/bin/vcfPileup    # vcfPileup to generate rich per-site information
 +
INFOCOLLECTOR = $(UMAKE_ROOT)/bin/infoCollector # create filtering statistics
 +
VCFMERGE = perl $(UMAKE_ROOT)/scripts/bams2vcfMerge.pl # merge multiple BAMs separated by chunk of genomes
 +
VCFCOOKER = $(UMAKE_ROOT)/bin/vcfCooker  # vcfCooker for filtering
 +
VCFSUMMARY = perl $(UMAKE_ROOT)/scripts/vcfSummary.pl # Get summary statistics of discovered site
 +
VCFSPLIT = perl $(UMAKE_ROOT)/scripts/vcfSplit.pl # split VCF into overlapping chunks for genotype refinement
 +
VCFPASTE = perl $(UMAKE_ROOT)/scripts/vcfPaste.pl # vcfPaste to generate filtered genotype VCF
 +
BEAGLE = java -Xmx4g -jar $(UMAKE_ROOT)/ext/beagle.20101226.jar seed=993478 gprobs=true niterations=50 lowmem=true # BEAGLE BINARY : NEED TO COPY BEAGLE TO $(UMAKE_ROOT)/ext DIRECTORY BEFORE RUNNING PIPELINE
 +
VCF2BEAGLE = perl $(UMAKE_ROOT)/scripts/vcf2Beagle.pl --PL # convert VCF (with PL tag) into beagle input
 +
BEAGLE2VCF = perl $(UMAKE_ROOT)/scripts/beagle2Vcf.pl # convert beagle output to VCF
 +
THUNDER = $(UMAKE_ROOT)/bin/thunderVCF -r 30 --phase --dosage --compact --inputPhased # MaCH/Thunder genotype refinement step
 +
LIGATEVCF = perl $(UMAKE_ROOT)/scripts/ligateVcf.pl # ligate multiple phased VCFs while resolving the phase between VCFs
 +
BGZIP = $(UMAKE_ROOT)/ext/bgzip  # NEED TO COPY BGZIP TO $(UMAKE_ROOT)/ext DIRECTORY BEFORE RUNNING PIPELINE
 +
TABIX = $(UMAKE_ROOT)/ext/tabix  # NEED TO COPY TABIX TO $(UMAKE_ROOT)/ext DIRECTORY BEFORE RUNNING PIPELINE
 +
###############################################################################
 +
## ARGUMENT FOR FILTERING
 +
###############################################################################
 +
SAMTOOLS_VIEW_FILTER = -q 20 -F 0x0704 # samtools view filter (-q by MQ, -F by flag)
 +
FILTER_MAX_SAMPLE_DP = 20  # Max Depth per Sample (20x default) -- will generate FILTER_MAX_TOTAL_DP automatically
 +
FILTER_MIN_SAMPLE_DP = 0.5 # Min Depth per Sample (0.5x defaul) -- will generate FILTER_MIN_TOTAL_DP automatically
 +
FILTER_ARGS = --write-vcf --filter --maxDP $(FILTER_MAX_TOTAL_DP) --minDP $(FILTER_MIN_TOTAL_DP) --maxAB 70 --maxSTR 20 --minSTR -20 --winIndel 5 --maxSTZ 5 --minSTZ -5 --maxAOI 5 # arguments for filtering (refer to vcfCooker for details)
 +
#############################################################################
 +
## RELATIVE DIRECTORY UNDER OUT_DIR
 +
#############################################################################
 +
BAM_GLF_DIR = glfs/bams  # BAM level GLF
 +
SM_GLF_DIR = glfs/samples # sample level GLF (after glfMerge if necessary)
 +
VCF_DIR = vcfs            # unfiltered and filtered VCF
 +
PVCF_DIR = pvcfs          # vcfPileup results
 +
SPLIT_DIR = split        # chunks split to multiple overlappingpieces
 +
BEAGLE_DIR = beagle      # beagle output
 +
THUNDER_DIR = thunder    # MaCH/thunder output
 +
GLF_INDEX = glfIndex.ped  # glfMultiples/glfExtract index file info
 +
#############################################################################
 +
## OTHER OPTIONS
 +
#############################################################################
 +
UNIT_CHUNK = 5000000      # Chunk size of SNP calling : 5Mb is default
 +
LD_NSNPS = 10000          # Chunk size of genotype refinement : 10,000 SNPs
 +
LD_OVERLAP = 1000        # Overlapping # of SNPs between chinks : 1,000 SNPs
 +
RUN_INDEX_FORCE = FALSE  # Regenerate BAM index file even if it exists
 +
MERGE_BEFORE_FILTER = FALSE # Merge across the chromosome before filtering
 +
NOBAQ_SUBSTRINGS = SOLID  # Avoid BAQ if the BAM file contains the substring
 +
ASSERT_BAM_EXIST = FALSE  # Check if BAM file exists
 +
#############################################################################
 +
## CLUSTER SETTING : CURRENTLY COMPATIBLE WITH MOSIX PLATFORM
 +
#############################################################################
 +
MOS_PREFIX =    # PREFIX FOR MOSIX COMMAND (BLANK IF UNUSED)
 +
MOS_NODES =      # COMMA-SEPARATED LIST OF NODES TO SUBMIT JOBS
 +
REMOTE_PREFIX =  # REMOTE_PREFIX : Set if cluster node see the directory differently (e.g. /net/mymachine/[original-dir])
 +
host8-223:umake-examples hmkang$ cat umake-example.conf | perl -lne 'chomp; print " $_"'
 +
##################################################################
 +
# UMAKE CONFIGURATION FILE
 +
# This configuration file contains run-time configuration of
 +
# UMAKE SNP calling pipeline
 +
###############################################################################
 +
## KEY ELEMENTS TO CONFIGURE : NEED TO MODIFY
 +
###############################################################################
 +
#UMAKE_ROOT = FULL_PATH_TO_UMAKE  ## e.g. /home/myid/code/umake
 +
#INPUT_ROOT = FULL_PATH_TO_CURRENT_DIR ## e.g. /home/myid/data/umake-examples
 +
#OUTPUT_ROOT = FULL_PATH_TO_OUTPUT_DIR ## e.g. /home/myid/data/umake-examples/out
 +
BAM_INDEX = $(INPUT_ROOT)/umake-example.index  # SAMPLE INDEX FILE (See documentation for detailed format)
 +
CHRS = 20              # List of chromosomes to call SNPs. For multiple chromosomes, separate by whitespace
 +
OUT_DIR = $(OUTPUT_ROOT)    # output directory
 +
OUT_PREFIX = umake-example  # prefix of output Makefile $(OUT_PREFIX).Makefile will be generated
 +
#PED_INDEX = $(INPUT_ROOT)/umake-example.ped    # SAMPLE PED FILE (required only for chrX calling)
 +
#
 +
###############################################################################
 +
## STEPS TO RUN : COMMENT OUT TO EXCLUDE CERTAIN STEPS
 +
##  --snpcall, --extract, --beagle, --thunder commands automatically set them
 +
###############################################################################
 +
#RUN_INDEX = TRUE        # create BAM index file
 +
#RUN_PILEUP = TRUE      # create GLF file from BAM
 +
#RUN_GLFMULTIPLES = TRUE # create unfiltered SNP calls
 +
#RUN_VCFPILEUP = TRUE    # create PVCF files using vcfPileup and run infoCollector
 +
#RUN_FILTER = TRUE      # filter SNPs using vcfCooker
 +
#RUN_SPLIT = TRUE        # split SNPs into chunks for genotype refinement
 +
#RUN_BEAGLE = TRUE  # BEAGLE - MUST SET AFTER FINISHING PREVIOUS STEPS
 +
#RUN_SUBSET = TRUE  # SUBSET FOR THUNDER - MAY BE SET WITH BEAGLE STEP TOGETHER
 +
#RUN_THUNDER = TRUE # THUNDER - MUST SET AFTER FINISHING PREVIOUS STEPS
 +
#
 +
###############################################################################
 +
## OPTIONS FOR GLFEXTRACT (GLFMULTIPLES, VCFPILEUP, FILTER MUST BE TURNED OFF)
 +
###############################################################################
 +
#RUN_EXTRACT = TRUE  # Instead of discovering SNPs, extract genotype liklihood in the site of VCF_EXTRACT
 +
#VCF_EXTRACT = # whole-genome (gzipped and tabixed) .vcf.gz file to extract the site information to genotype (such as 1000 Genomes site list)
 +
#
 +
###############################################################################
 +
## OPTIONS FOR EXOME/TARGETED SEQUENCING : COMMENT OUT IF WHOLE GENOME SEQUENCING
 +
###############################################################################
 +
WRITE_TARGET_LOCI = TRUE  # FOR TARGETED SEQUENCING ONLY -- Write loci file when performing pileup
 +
UNIFORM_TARGET_BED = $(INPUT_ROOT)/umake-example.bed # Targeted sequencing : When all individuals has the same target. Otherwise, comment it out
 +
OFFSET_OFF_TARGET = 50 # Extend target by given # of bases
 +
MULTIPLE_TARGET_MAP =  # Target per individual : Each line contains [SM_ID] [TARGET_BED]
 +
TARGET_DIR = target    # Directory to store target information
 +
SAMTOOLS_VIEW_TARGET_ONLY = TRUE # When performing samtools view, exclude off-target regions (may make command line too long)
 +
#
 +
###############################################################################
 +
## RESOURCE FILES : Download the full resources for full genome calling
 +
###############################################################################
 +
REF = $(INPUT_ROOT)/data/ref/human_g1k_v37_chr20.fa # Reference FASTA sequence. Note that the FASTA file in the example package is only chr20.
 +
INDEL_PREFIX = $(INPUT_ROOT)/data/indels/1kg.pilot_release.merged.indels.sites.hg19 # 1000 Genomes Pilot 1 indel VCF prefix
 +
DBSNP_PREFIX =  $(INPUT_ROOT)/data/dbsnp/dbsnp_129_b37.rod # dbSNP file prefix
 +
HM3_PREFIX =  $(INPUT_ROOT)/data/HapMap/hapmap3_r3_b37_fwd.consensus.qc.poly # HapMap3 polymorphic site prefix
 +
#
 +
###############################################################################
 +
## BINARIES
 +
###############################################################################
 +
SAMTOOLS_FOR_PILEUP = $(UMAKE_ROOT)/bin/samtools-hybrid # for samtools pileup
 +
SAMTOOLS_FOR_OTHERS = $(UMAKE_ROOT)/bin/samtools-hybrid # for samtools view and calmd
 +
GLFMERGE = $(UMAKE_ROOT)/bin/glfMerge # glfMerge when multiple BAMs exist per indvidual
 +
GLFMULTIPLES = $(UMAKE_ROOT)/bin/glfMultiples --minMapQuality 0 --minDepth 1 --maxDepth 10000000 --uniformTsTv --smartFilter # glfMultiples and options
 +
GLFEXTRACT = $(UMAKE_ROOT)/bin/glfExtract  # glfExtract for obtaining VCF for known sites
 +
VCFPILEUP = $(UMAKE_ROOT)/bin/vcfPileup    # vcfPileup to generate rich per-site information
 +
INFOCOLLECTOR = $(UMAKE_ROOT)/bin/infoCollector # create filtering statistics
 +
VCFMERGE = perl $(UMAKE_ROOT)/scripts/bams2vcfMerge.pl # merge multiple BAMs separated by chunk of genomes
 +
VCFCOOKER = $(UMAKE_ROOT)/bin/vcfCooker  # vcfCooker for filtering
 +
VCFSUMMARY = perl $(UMAKE_ROOT)/scripts/vcfSummary.pl # Get summary statistics of discovered site
 +
VCFSPLIT = perl $(UMAKE_ROOT)/scripts/vcfSplit.pl # split VCF into overlapping chunks for genotype refinement
 +
VCFPASTE = perl $(UMAKE_ROOT)/scripts/vcfPaste.pl # vcfPaste to generate filtered genotype VCF
 +
BEAGLE = java -Xmx4g -jar $(UMAKE_ROOT)/ext/beagle.20101226.jar seed=993478 gprobs=true niterations=50 lowmem=true # BEAGLE BINARY : NEED TO COPY BEAGLE TO $(UMAKE_ROOT)/ext DIRECTORY BEFORE RUNNING PIPELINE
 +
VCF2BEAGLE = perl $(UMAKE_ROOT)/scripts/vcf2Beagle.pl --PL # convert VCF (with PL tag) into beagle input
 +
BEAGLE2VCF = perl $(UMAKE_ROOT)/scripts/beagle2Vcf.pl # convert beagle output to VCF
 +
THUNDER = $(UMAKE_ROOT)/bin/thunderVCF -r 30 --phase --dosage --compact --inputPhased # MaCH/Thunder genotype refinement step
 +
LIGATEVCF = perl $(UMAKE_ROOT)/scripts/ligateVcf.pl # ligate multiple phased VCFs while resolving the phase between VCFs
 +
BGZIP = $(UMAKE_ROOT)/ext/bgzip  # NEED TO COPY BGZIP TO $(UMAKE_ROOT)/ext DIRECTORY BEFORE RUNNING PIPELINE
 +
TABIX = $(UMAKE_ROOT)/ext/tabix  # NEED TO COPY TABIX TO $(UMAKE_ROOT)/ext DIRECTORY BEFORE RUNNING PIPELINE
 +
#
 +
###############################################################################
 +
## ARGUMENT FOR FILTERING
 +
###############################################################################
 +
SAMTOOLS_VIEW_FILTER = -q 20 -F 0x0704 # samtools view filter (-q by MQ, -F by flag)
 +
FILTER_MAX_SAMPLE_DP = 20  # Max Depth per Sample (20x default) -- will generate FILTER_MAX_TOTAL_DP automatically
 +
FILTER_MIN_SAMPLE_DP = 0.5 # Min Depth per Sample (0.5x defaul) -- will generate FILTER_MIN_TOTAL_DP automatically
 +
FILTER_ARGS = --write-vcf --filter --maxDP $(FILTER_MAX_TOTAL_DP) --minDP $(FILTER_MIN_TOTAL_DP) --maxAB 70 --maxSTR 20 --minSTR -20 --winIndel 5 --maxSTZ 5 --minSTZ -5 --maxAOI 5 # arguments for filtering (refer to vcfCooker for details)
 +
#
 +
#############################################################################
 +
## RELATIVE DIRECTORY UNDER OUT_DIR
 +
#############################################################################
 +
BAM_GLF_DIR = glfs/bams  # BAM level GLF
 +
SM_GLF_DIR = glfs/samples # sample level GLF (after glfMerge if necessary)
 +
VCF_DIR = vcfs            # unfiltered and filtered VCF
 +
PVCF_DIR = pvcfs          # vcfPileup results
 +
SPLIT_DIR = split        # chunks split to multiple overlappingpieces
 +
BEAGLE_DIR = beagle      # beagle output
 +
THUNDER_DIR = thunder    # MaCH/thunder output
 +
GLF_INDEX = glfIndex.ped  # glfMultiples/glfExtract index file info
 +
#
 +
#############################################################################
 +
## OTHER OPTIONS
 +
#############################################################################
 +
UNIT_CHUNK = 5000000      # Chunk size of SNP calling : 5Mb is default
 +
LD_NSNPS = 10000          # Chunk size of genotype refinement : 10,000 SNPs
 +
LD_OVERLAP = 1000        # Overlapping # of SNPs between chinks : 1,000 SNPs
 +
RUN_INDEX_FORCE = FALSE  # Regenerate BAM index file even if it exists
 +
MERGE_BEFORE_FILTER = FALSE # Merge across the chromosome before filtering
 +
NOBAQ_SUBSTRINGS = SOLID  # Avoid BAQ if the BAM file contains the substring
 +
ASSERT_BAM_EXIST = FALSE  # Check if BAM file exists
 +
#
 +
#############################################################################
 +
## CLUSTER SETTING : CURRENTLY COMPATIBLE WITH MOSIX PLATFORM
 +
#############################################################################
 +
MOS_PREFIX =    # PREFIX FOR MOSIX COMMAND (BLANK IF UNUSED)
 +
MOS_NODES =      # COMMA-SEPARATED LIST OF NODES TO SUBMIT JOBS
 +
REMOTE_PREFIX =  # REMOTE_PREFIX : Set if cluster node see the directory differently (e.g. /net/mymachine/[original-dir])
 +
 +
    
== Software Components ==
 
== Software Components ==
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/3299"

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