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Revision as of 18:04, 23 October 2014
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= Running the GotCloud Variant Calling Pipeline =
== Running the GotCloud Variant Calling Pipeline ==
The variant calling pipeline (umake) is run using <code>gotcloud snpcall</code> and <code>gotcloud ldrefine</code>.
The variant calling pipeline (umake) is run using <code>gotcloud snpcall</code> and <code>gotcloud ldrefine</code>.
==Running the Automatic Test==
===Running the Automatic Test===
The automatic test runs the variant calling pipeline on a small test set and checks the results against expected results validating that GotCloud is installed correctly.
The automatic test runs the variant calling pipeline on a small test set and checks the results against expected results validating that GotCloud is installed correctly.
** 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.
= Overview of Variant Calling Pipeline Steps =
== Overview of Variant Calling Pipeline Steps ==
Here is an overview of the Variant Calling Pipeline:
Here is an overview of the Variant Calling Pipeline:
For more information on the filters applied during the Variant Calling Pipeline, see, [[GotCloud: Filters]].
For more information on the filters applied during the Variant Calling Pipeline, see, [[GotCloud: Filters]].
= Input Data=
== Input Data==
* [[#BAM Files|Aligned/Processed/Recalibrated BAM files]]
* [[#BAM Files|Aligned/Processed/Recalibrated BAM files]]
* [[#BAM List File|BAM list file containing Sample IDs & BAM file names]]
* [[#BAM List File|BAM list file containing Sample IDs & BAM file names]]
* (Optional) [[#Configuration File|Configuration file to override default options]]
* (Optional) [[#Configuration File|Configuration file to override default options]]
== BAM Files ==
=== 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 automatically done 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 automatically done as part of the [[Alignment Pipeline]] of GotCloud.
== BAM List File ==
=== BAM List File ===
* Automatically created when running the GotCloud [[Alignment Pipeline]]
* Automatically created when running the GotCloud [[Alignment Pipeline]]
* Each line of the BAM list file represents a single individual
* Each line of the BAM list file represents a single individual
*** 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.
== Reference Files ==
=== Reference Files ===
See [[GotCloud: Genetic Reference and Resource Files]] for detailed information about the multiple required reference files for the variant calling pipeline, including:
See [[GotCloud: Genetic Reference and Resource Files]] for detailed information about the multiple required reference files for the variant calling pipeline, including:
* How to obtain default references
* How to obtain default references
* [[GotCloud: Genetic Reference and Resource Files#INDEL VCF File(s)|INDEL VCF File(s)]]
* [[GotCloud: Genetic Reference and Resource Files#INDEL VCF File(s)|INDEL VCF File(s)]]
== Configuration File ==
=== Configuration File ===
{{:GotCloud: Configuration}}
{{:GotCloud: Configuration}}
===Additional Required User Config Files Settings===
====Additional 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
===Targeted/Exome Sequencing Settings===
====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
=== Chromosome X Calling ===
==== Chromosome X Calling ====
Making calls on the X chromosome requires the user to specifty a PED file with sex information.
Making calls on the X chromosome requires the user to specifty a PED file with sex information.
* PED_INDEX = pedfile.ped
* PED_INDEX = pedfile.ped
== Example Configuration File ==
=== Example Configuration File ===
Example configuration file where reference files happen to be stored in /path/reference, and bam index file in path/freeze5
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
CHRS = 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22
DBSNP_VCF = /path/reference/dbsnp_135.b37.sites.vcf.gz ### dbSNP 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 ==
Running variant calling is straightforward:
Running variant calling is straightforward:
== Running on a Cluster ==
=== 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:
BATCH_TYPE = batch_type
BATCH_TYPE = batch_type
Here's the same configuration file we used above but now made to run on a cluster computer with MOSIX.
Here's the same configuration file we used above but now made to run on a cluster computer with MOSIX.
== Example Configuration File ==
=== Example Configuration File ===
CHRS = 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22
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
BAM_INDEX = /path/freeze5/freeze5.bam.index
BATCH_OPTS = -j10,11,12,13 ### Specify available MOSIX compute nodes
BATCH_OPTS = -j10,11,12,13 ### Specify available MOSIX compute nodes
= Results =
== Results ==
If there is a failure, you should see a message like:
If there is a failure, you should see a message like:
