Mercurial > repos > jjohnson > gatk2
diff variant_recalibrator.xml @ 31:a5c55503d196 draft
variant_recalibrator Omit --read_filter for MalformedReadFilter since it included by default, allows --filter_mismatching_base_and_quals to be set
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Thu, 28 Feb 2013 12:44:55 -0600 |
| parents | 6ef8eb568700 |
| children | 76f8ca47b810 |
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--- a/variant_recalibrator.xml Tue Feb 19 21:04:33 2013 -0600 +++ b/variant_recalibrator.xml Thu Feb 28 12:44:55 2013 -0600 @@ -4,6 +4,7 @@ <requirement type="package" version="2.3">gatk</requirement> </requirements> <command interpreter="python">gatk2_wrapper.py + #set default_read_filters = ['DuplicateReadFilter', 'FailsVendorQualityCheckFilter', 'NotPrimaryAlignmentFilter', 'MalformedReadFilter', 'UnmappedReadFilter'] --max_jvm_heap_fraction "1" --stdout "${output_log}" #for $var_count, $variant in enumerate( $reference_source.variants ): @@ -52,7 +53,10 @@ #end for -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"' #for $read_filter in $gatk_param_type.read_filter: - -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}" + -p ' + #if ${read_filter.read_filter_type.read_filter_type_selector} not in $default_read_filters: + --read_filter "${read_filter.read_filter_type.read_filter_type_selector}" + #end_if ###raise Exception( str( dir( $read_filter ) ) ) #for $name, $param in $read_filter.read_filter_type.iteritems(): #if $name not in [ "__current_case__", "read_filter_type_selector" ]: