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Revision as of 17:30, 21 March 2013
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Back to parent: [[GotCloud]]
Back to parent: [[GotCloud]]
The variant calling pipeline (umake) is run using <code>gotcloud snpcall</code> and <code>gotcloud ldrefine</code>. <code>gotcloud</code> is found under <code>gotcloud/</code>.
The variant calling pipeline (umake) is run using <code>gotcloud snpcall</code> and <code>gotcloud ldrefine</code>. <code>gotcloud</code> is found under <code>gotcloud/</code>.
==Running the Automatic Test==
The automatic test runs the variant calling pipeline on a small testset and checks the results against expected results validating that GotCloud is installed correctly.
The automatic test runs the variant calling pipeline on a small testset and checks the results against expected results validating that GotCloud is installed correctly.
If you see "Successfully ran the test case, congratulations!", then you are ready to align samples.
If you see "Successfully ran the test case, congratulations!", then you are ready to align samples.
= Overview of Variant Calling Pipeline Steps =
Here is an overview of the Variant Calling Pipeline:
Here is an overview of the Variant Calling Pipeline:
= Input Data=
*Aligned/Processed/Recalibrated BAM files
*Aligned/Processed/Recalibrated BAM files
*Index file containing Sample IDs & BAM file names
*Index file containing Sample IDs & BAM file names
*(Optional) Configuration file to override default options
*(Optional) Configuration file to override default options
== BAM files ==
The BAM files need to be duplicate-marked and base-quality recalibrated in order to obtain high quality SNP calls. Generating these BAM files from original FASTQs is documented elsewhere as part of the [[Alignment Pipeline]] of gotCloud.
The BAM files need to be duplicate-marked and base-quality recalibrated in order to obtain high quality SNP calls. Generating these BAM files from original FASTQs is documented elsewhere as part of the [[Alignment Pipeline]] of gotCloud.
== Index File ==
Each line of the index file represents each individual under the following format. Note that multiple BAMs per individual may be provided.
Each line of the 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] ...
: # BAM File N
: # BAM File N
== Reference Files ==
The variant calling pipeline requires multiple reference files in order to work correctly.
The variant calling pipeline requires multiple reference files in order to work correctly.
HM3_PREFIX = path/hapmap3.qc.poly
HM3_PREFIX = path/hapmap3.qc.poly
== Configuration File ==
Configuration file contains the run-time options including the software binaries and command line arguments. A default configuration file is automatically loaded. Users must specify their own configuration file specifying just the values different than the defaults.
Configuration file contains the run-time options including the software binaries and command line arguments. A default configuration file is automatically loaded. Users must specify their own configuration file specifying just the values different than the defaults.
Where KEY is the item being set and value is its new 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:
The following Config File Settings must be specified by the user:
* CHRS = space separated list of chromosomes you want
* CHRS = space separated list of chromosomes you want
* BAM_INDEX = path to the Index File of BAMs
* 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:
The following Command-Line or Config File Settings must be specified by the user:
* --outdir/OUT_DIR= path to desired output directory
* --outdir/OUT_DIR= path to desired output directory
===Targeted/Exome Sequencing Settings===
If you are running Targeted/Exome Sequencing, the user should specify:
If you are running Targeted/Exome Sequencing, the user should specify:
* Write loci file when performing pileup
* Write loci file when performing pileup
** OFFSET_OFF_TARGET = 50
** OFFSET_OFF_TARGET = 50
=== Configure Reference Files ===
See [[#Reference Files| Reference Files]] for information on how to specify the reference files.
See [[#Reference Files| Reference Files]] for information on how to specify the reference files.
=== Chromosome X Calling ===
* PED_INDEX = pedfile.ped
* PED_INDEX = pedfile.ped
= Running =
Running variant calling is straightforward:
Running variant calling is straightforward:
== Running on a Cluster ==
To run on the Cluster, the following settings need to be added to the configuration file:
To run on the Cluster, the following settings need to be added to the configuration file:
= Results =
If there is a failure, you should see a message like:
If there is a failure, you should see a message like:
