Mercurial > repos > jjohnson > gatk2
changeset 38:1061731ba6ed draft
Update options for UnifiedGenotyper p_nonref_model for version 2.3
author | Jim Johnson <jj@umn.edu> |
---|---|
date | Mon, 04 Mar 2013 21:37:30 -0600 (2013-03-05) |
parents | dd9f8ea2b718 |
children | fab099dde911 |
files | unified_genotyper.xml |
diffstat | 1 files changed, 3 insertions(+), 3 deletions(-) [+] |
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--- a/unified_genotyper.xml Fri Mar 01 12:43:41 2013 -0600 +++ b/unified_genotyper.xml Mon Mar 04 21:37:30 2013 -0600 @@ -443,8 +443,8 @@ </when> <when value="advanced"> <param name="p_nonref_model" type="select" label="Non-reference probability calculation model to employ" help="-pnrm,--p_nonref_model &lt;p_nonref_model&gt;"> - <option value="EXACT" selected="True">EXACT</option> - <option value="GRID_SEARCH">GRID_SEARCH</option> + <option value="EXACT_GENERAL_PLOIDY" selected="True">EXACT_GENERAL_PLOIDY (supports any sample ploidy)</option> + <option value="EXACT_REFERENCE">EXACT_REFERENCE (multi-allelic EXACT model. Extremely slow for many alternate alleles)</option> </param> <param name="heterozygosity" type="float" value="1e-3" label="Heterozygosity value used to compute prior likelihoods for any locus" help="-hets,--heterozygosity &lt;heterozygosity&gt;" /> <param name="pcr_error_rate" type="float" value="1e-4" label="The PCR error rate to be used for computing fragment-based likelihoods" help="-pcr_error,--pcr_error_rate &lt;pcr_error_rate&gt;" /> @@ -598,7 +598,7 @@ **Settings**:: genotype_likelihoods_model Genotype likelihoods calculation model to employ -- BOTH is the default option, while INDEL is also available for calling indels and SNP is available for calling SNPs only (SNP|INDEL|BOTH) - p_nonref_model Non-reference probability calculation model to employ -- EXACT is the default option, while GRID_SEARCH is also available. (EXACT|GRID_SEARCH) + p_nonref_model Non-reference probability calculation model to employ -- EXACT_GENERAL_PLOIDY is the default option, while EXACT_REFERENCE is also available. (EXACT_INDEPENDENT,EXACT_REFERENCE,EXACT_ORIGINAL,EXACT_GENERAL_PLOIDY) heterozygosity Heterozygosity value used to compute prior likelihoods for any locus pcr_error_rate The PCR error rate to be used for computing fragment-based likelihoods genotyping_mode Should we output confident genotypes (i.e. including ref calls) or just the variants? (DISCOVERY|GENOTYPE_GIVEN_ALLELES)