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| === Configuration File === | | === Configuration File === |
| + | A default configuration file is automatically loaded. Users must specify their own configuration file specifying just the values different than the defaults. |
| + | |
| + | Comments begin with a <code>#</code> |
| + | |
| + | Format: KEY = value |
| + | |
| + | Where KEY is the item being set and value is its new value |
| + | |
| + | |
| + | ====Required User Config Files Settings==== |
| + | The following Config File Settings must be specified by the user: |
| + | * CHRS = # space separated list of chromosomes you want |
| + | * BAM_INDEX = # path to the Index File of BAMs |
| + | |
| + | ====Required on Command-Line or in Config File==== |
| + | The following Command-Line or Config File Settings must be specified by the user: |
| + | * --outdir/OUTDIR= # path to desired output directory |
| + | |
| + | ====Targeted/Exome Sequencing Settings==== |
| + | If you are running Targeted/Exome Sequencing, the user should specify: |
| + | * Write loci file when performing pileup |
| + | ** WRITE_TARGET_LOCI = TRUE |
| + | * Specify the directory to store target information, for example: targetDir |
| + | ** TARGET_DIR = targetDir |
| + | |
| + | If all individuals have the same target: |
| + | * Specify the single bed file, for example: target.bed |
| + | ** UNIFORM_TARGET_BED = target.bed |
| + | |
| + | If not all individuals have the same target: |
| + | * Specify the file containing the sample id -> bed map, for example: targetMap.txt |
| + | ** MULTIPLE_TARGET_MAP = targetMap.txt |
| + | *** Each line of the file contains [SM_ID] [TARGET_BED] |
| + | |
| + | Optional Settings: |
| + | * Extend the target region by a given number of bases, for example: 50 |
| + | ** OFFSET_OFF_TARGET = 50 |
| + | * Exclude off-target regions when using samtools view (may make command line too long) |
| + | ** SAMTOOLS_VIEW_TARGET_ONLY = TRUE |
| + | |
| + | |
| + | ==== Reference Files ==== |
| + | * Reference Sequence in fasta format. |
| + | ** REF = path/file.fa |
| + | * Indel VCF File Prefix |
| + | ** INDEL_PREFIX = path/indels.sites.hg19 |
| + | ** path/ contains indels.sites.hg19.chr20.vcf for each chromosome being processed |
| + | * DBSNP File Prefix |
| + | ** DBSNP_PREFIX = path/dbsnp_135_b37.rod |
| + | ** path/ contains dbsnp_135_b37.rod.chr20.map for each chromosome being processed |
| + | * HapMap3 polymorphic site prefix |
| + | ** HM3_PREFIX = path/hapmap3.qc.poly |
| + | ** path/ contains hapmap3.qc.poly.chr20.bim & hapmap3.qc.poly.chr20.frq for each chromosome being processed |
| + | |
| + | Can be downloaded from: [[ftp://share.sph.umich.edu/1000genomes/umake-resources/ | FTP Download of Full Resource Files]] |
| + | |
| + | INDEL_PREFIX = $(UMAKE_ROOT)/ref/indels/1kg.pilot_release.merged.indels.sites.hg19 # 1000 Genomes Pilot 1 indel VCF prefix |
| + | DBSNP_PREFIX = $(UMAKE_ROOT)/ref/dbSNP/dbsnp_135_b37.rod # dbSNP file prefix |
| + | HM3_PREFIX = $(UMAKE_ROOT)/ref/HapMap3/hapmap3_r3_b37_fwd.consensus.qc.poly # HapMap3 polymorphic site prefix |
| + | |
| + | ==== Chromosome X Calling ==== |
| + | * PED_INDEX = pedfile.ped |
| + | |
| | | |
| == Running == | | == Running == |