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GotCloud: Variant Calling Pipeline (view source)

Revision as of 18:54, 30 March 2015

421 bytes added ,  18:54, 30 March 2015
→‎Running the Automatic Test
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** If you see <code>Successfully ran the test case, congratulations!</code>, then you are ready to run snpcall on your own samples.
 
** If you see <code>Successfully ran the test case, congratulations!</code>, then you are ready to run snpcall on your own samples.
 
*Run <code>ldrefine</code> pipeline test:
 
*Run <code>ldrefine</code> pipeline test:
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  gotcloud snpcall --test OUTPUT_DIR
+
  gotcloud ldrefine --test OUTPUT_DIR
 
** Where <code>OUTPUT_DIR</code> is the directory where you want to store the test results
 
** Where <code>OUTPUT_DIR</code> is the directory where you want to store the test results
 
** If you see <code>Successfully ran the test case, congratulations!</code>, then you are ready to run ldrefine on your own samples.
 
** If you see <code>Successfully ran the test case, congratulations!</code>, then you are ready to run ldrefine on your own samples.
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*** only used by Thunder (part of ldrefine pipeline)
 
*** only used by Thunder (part of ldrefine pipeline)
 
*** if all samples are from the same population, population label can be skipped or you can just specify <code>ALL</code> for the population label for each sample.
 
*** if all samples are from the same population, population label can be skipped or you can just specify <code>ALL</code> for the population label for each sample.
 +
 +
The path to the BAM List file is defaulted to the <code>outputDirectory/bam.list</code>.  It can be overridden by setting <code>--bamlist</code>, <code>--bam_list</code>, or <code>--list</code> on the command-line or by setting BAM_LIST in your configuration file to the path to the BAM List File.  See [[#Required_Options|Required Options]] for more information.
    
=== Reference Files ===
 
=== Reference Files ===
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{{:GotCloud: Configuration}}
 
{{:GotCloud: Configuration}}
   −
====Additional Required User Config Files Settings====
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See [[#Variant Calling Command-line Options/Configuration Settings|Variant Calling Command-line Options/Configuration Settings]] for more information on Configuration options.
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The following Config File Settings must be specified by the user:
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* CHRS = space separated list of chromosomes you want
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==== Example Configuration File ====
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* BAM_INDEX = path to the Index File of BAMs
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Example configuration file where reference files happen to be stored in /path/reference, and bam index file in path/freeze5
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CHRS = 20 22
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BAM_LIST = /path/freeze5.bam.list
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OUT_DIR = /path/freeze5/output
 +
REF_DIR = /path/reference/
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REF = $(REF_DIR)/hs37d5.fa
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INDEL_PREFIX = $(REF_DIR)/1kg.pilot_release.merged.indels.sites.hg19
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HM3_VCF = $(REF_DIR)/hapmap3_r3_b37.sites.vcf.gz
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DBSNP_VCF = $(REF_DIR)/dbsnp_135.b37.sites.vcf.gz
 +
 
   −
====Targeted/Exome Sequencing Settings====
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== Variant Calling Command-line Options/Configuration Settings ==
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If you are running Targeted/Exome Sequencing, the user should specify:
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{{:GotCloud: Variant Calling Options}}
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* Write loci file when performing pileup
  −
** WRITE_TARGET_LOCI = TRUE
  −
* Specify the output sub-directory to store target information, for example: targetDir
  −
** Should not be a full path as this will co under the OUT_DIR directory.
  −
** 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:
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== Use Cases & Recommended Settings ==
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* Specify the file containing the sample id -> bed map, for example: targetMap.txt
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=== Single Sample Processing ===
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** MULTIPLE_TARGET_MAP = targetMap.txt
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To run single sample processing we recommend adding the following settings to your configuration file:
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*** Each line of the file contains [SM_ID] [TARGET_BED]
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UNIT_CHUNK = 20000000
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MODEL_GLFSINGLE = TRUE
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MODEL_SKIP_DISCOVER = FALSE
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MODEL_AF_PRIOR = TRUE
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VCF_EXTRACT = $(REF_DIR)/snpOnly.vcf.gz
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EXT = $(REF_DIR)/ALL.chrCHR.phase3.combined.sites.unfiltered.vcf.gz $(REF_DIR)/chrCHR.filtered.sites.vcf.gz
   −
Optional Settings:
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Explanation of these settings:
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* Extend the target region by a given number of bases, for example: 50
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* <code>UNIT_CHUNK</code> - since this is only 1 sample, process larger regions at a time than default
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** OFFSET_OFF_TARGET = 50
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* <code>MODEL_GLFSINGLE</code> - single sample, so model glfsingle
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* <code>MODEL_SKIP_DISCOVER</code> - do not skip the variant discovery step
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* <code>MODEL_AF_PRIOR</code> - use AF prior for genotyping
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* <code>VCF_EXTRACT</code> - VCF file to use for extracting the site information to genotype
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**  This file is included in the latest reference release: [[GotCloud:_Genetic_Reference_and_Resource_Files#hs37d5-db142|hs37d5-db142]]
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* <code>EXT</code> - VCF reference files to use for the external filtering
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** These files are included in the latest reference release: [[GotCloud:_Genetic_Reference_and_Resource_Files#hs37d5-db142|hs37d5-db142]]
   −
==== Chromosome X Calling ====
  −
Making calls on the X chromosome requires the user to specifty a PED file with sex information.
  −
* PED_INDEX = pedfile.ped
     −
=== Example Configuration File ===
  −
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
  −
BAM_INDEX = /path/freeze5/freeze5.bam.index  ### The BAM index file described above
  −
OUT_DIR = /path/freeze5/output              ### Directory in which to put all gotcloud output
  −
REF = /path/reference/hs37d5.fa              ### Reference sequence
  −
INDEL_PREFIX = /path/reference/1kg.pilot_release.merged.indels.sites.hg19  ### Known indel sites
  −
HM3_VCF = /path/reference/hapmap3_r3_b37.sites.vcf.gz    ### HapMap variants (requires tabix index file in same directory)
  −
DBSNP_VCF = /path/reference/dbsnp_135.b37.sites.vcf.gz  ### dbSNP variants (requires tabix index file in same directory)
      
== Running ==
 
== Running ==
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* Replace <code>2</code> following <code>--numjobs</code> with the number of jobs to be run in parallel
 
* Replace <code>2</code> following <code>--numjobs</code> with the number of jobs to be run in parallel
 
* If <code>OUT_DIR</code> is not defined in the configuration file, add <code>--outdir</code> followed by the path to the user's desired output directory.
 
* If <code>OUT_DIR</code> is not defined in the configuration file, add <code>--outdir</code> followed by the path to the user's desired output directory.
−
      
=== Running on a Cluster ===
 
=== Running on a Cluster ===
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See [[#Cluster Configuration|Cluster Configuration]] settings for information on how to run on a cluster.
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See [[#Cluster Configuration|Cluster Configuration]] for information on how to configure GotCloud to run on a cluster.
    
== Results ==
 
== Results ==
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* glfs with a bams & samples subdirectory
 
* glfs with a bams & samples subdirectory
 
* pvcfs with a subdirectory per chromosome and then per region
 
* pvcfs with a subdirectory per chromosome and then per region
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* split with a subdirectory per chromosome
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* '''split''' with a subdirectory per chromosome
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* vcfs with a subdirectory per chromosome
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* '''vcfs''' with a subdirectory per chromosome
 
* (optionally your target directory)
 
* (optionally your target directory)
   −
Under the vcf/chrXX directory, there should be:
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Under the '''vcf/chrXX''' directory, there should be:
 
* chrXX.filtered.sites.vcf
 
* chrXX.filtered.sites.vcf
 
* chrXX.filtered.sites.vcf.norm.log
 
* chrXX.filtered.sites.vcf.norm.log
 
* chrXX.filtered.sites.vcf.summary
 
* chrXX.filtered.sites.vcf.summary
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* chrXX.filtered.vcf.gz
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* '''chrXX.filtered.vcf.gz''' - final filtered variant call file
 
* chrXX.filtered.vcf.gz.OK
 
* chrXX.filtered.vcf.gz.OK
 
* chrXX.filtered.vcf.gz.tbi
 
* chrXX.filtered.vcf.gz.tbi
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The filtered is the merged.vcf after it has been run through filters and is marked with PASS/FAIL.
 
The filtered is the merged.vcf after it has been run through filters and is marked with PASS/FAIL.
   −
Under the split/chrXX directory, there should be:
+
Under the '''split/chrXX''' directory, there should be:
 
* chrXX.filtered.PASS.split.[N].vcf.gz
 
* chrXX.filtered.PASS.split.[N].vcf.gz
 
* chrXX.filtered.PASS.split.err
 
* chrXX.filtered.PASS.split.err
 
* chrXX.filtered.PASS.split.vcflist
 
* chrXX.filtered.PASS.split.vcflist
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* chrXX.filtered.PASS.gz
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* '''chrXX.filtered.PASS.gz''' - final variant call file with only PASS variants
 
* subset.OK
 
* subset.OK
Kleckner
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