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Revision as of 18:54, 30 March 2015
, 18:54, 30 March 2015→Running the Automatic Test
** 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:
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.
*** 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 ===
== Variant Calling Command-line Options/Configuration Settings ==
== Variant Calling Command-line Options/Configuration Settings ==
{{:GotCloud: Variant Calling Options}}
{{:GotCloud: Variant Calling Options}}
== Use Cases & Recommended Settings ==
=== Single Sample Processing ===
To run single sample processing we recommend adding the following settings to your configuration file:
UNIT_CHUNK = 20000000
MODEL_GLFSINGLE = TRUE
MODEL_SKIP_DISCOVER = FALSE
MODEL_AF_PRIOR = TRUE
VCF_EXTRACT = $(REF_DIR)/snpOnly.vcf.gz
EXT = $(REF_DIR)/ALL.chrCHR.phase3.combined.sites.unfiltered.vcf.gz $(REF_DIR)/chrCHR.filtered.sites.vcf.gz
Explanation of these settings:
* <code>UNIT_CHUNK</code> - since this is only 1 sample, process larger regions at a time than default
* <code>MODEL_GLFSINGLE</code> - single sample, so model glfsingle
* <code>MODEL_SKIP_DISCOVER</code> - do not skip the variant discovery step
* <code>MODEL_AF_PRIOR</code> - use AF prior for genotyping
* <code>VCF_EXTRACT</code> - VCF file to use for extracting the site information to genotype
** This file is included in the latest reference release: [[GotCloud:_Genetic_Reference_and_Resource_Files#hs37d5-db142|hs37d5-db142]]
* <code>EXT</code> - VCF reference files to use for the external filtering
** These files are included in the latest reference release: [[GotCloud:_Genetic_Reference_and_Resource_Files#hs37d5-db142|hs37d5-db142]]
* 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
* split with a subdirectory per chromosome
* '''split''' with a subdirectory per chromosome
* vcfs with a subdirectory per chromosome
* '''vcfs''' with a subdirectory per chromosome
* (optionally your target directory)
* (optionally your target directory)
Under the vcf/chrXX directory, there should be:
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
* chrXX.filtered.vcf.gz
* '''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
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
* chrXX.filtered.PASS.gz
* '''chrXX.filtered.PASS.gz''' - final variant call file with only PASS variants
* subset.OK
* subset.OK
