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− | = Running the GotCloud Variant Calling Pipeline = | + | == Running the GotCloud Variant Calling Pipeline == |
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| 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>. |
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− | ==Running the Automatic Test== | + | ===Running the Automatic Test=== |
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| 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. |
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| ** 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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− | = 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: |
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| 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]]. |
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− | = 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]] |
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| * (Optional) [[#Configuration File|Configuration file to override default options]] | | * (Optional) [[#Configuration File|Configuration file to override default options]] |
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− | == 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. |
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− | == 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 |
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| *** 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. |
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− | == 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 |
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| * [[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)]] |
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− | == Configuration File == | + | === Configuration File === |
| {{:GotCloud: Configuration}} | | {{:GotCloud: Configuration}} |
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− | ===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 |
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− | ===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 |
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| ** OFFSET_OFF_TARGET = 50 | | ** OFFSET_OFF_TARGET = 50 |
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− | === 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 |
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− | == 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 |
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| 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) |
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− | = Running = | + | == Running == |
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| Running variant calling is straightforward: | | Running variant calling is straightforward: |
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− | == 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 |
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| 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 |
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| BATCH_OPTS = -j10,11,12,13 ### Specify available MOSIX compute nodes | | BATCH_OPTS = -j10,11,12,13 ### Specify available MOSIX compute nodes |
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− | = Results = | + | == Results == |
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| If there is a failure, you should see a message like: | | If there is a failure, you should see a message like: |