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Revision as of 14:23, 6 March 2015
, 14:23, 6 March 2015→Running
== 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]]
