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comparison variant_recalibrator.xml @ 31:a5c55503d196 draft

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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
comparison
equal deleted inserted replaced
30:0ca0c3270e32 31:a5c55503d196
2 <description></description> 2 <description></description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.3">gatk</requirement> 4 <requirement type="package" version="2.3">gatk</requirement>
5 </requirements> 5 </requirements>
6 <command interpreter="python">gatk2_wrapper.py 6 <command interpreter="python">gatk2_wrapper.py
7 #set default_read_filters = ['DuplicateReadFilter', 'FailsVendorQualityCheckFilter', 'NotPrimaryAlignmentFilter', 'MalformedReadFilter', 'UnmappedReadFilter']
7 --max_jvm_heap_fraction "1" 8 --max_jvm_heap_fraction "1"
8 --stdout "${output_log}" 9 --stdout "${output_log}"
9 #for $var_count, $variant in enumerate( $reference_source.variants ): 10 #for $var_count, $variant in enumerate( $reference_source.variants ):
10 -d "--input:input_${var_count},%(file_type)s" "${variant.input_variants}" "${variant.input_variants.ext}" "input_variants_${var_count}" 11 -d "--input:input_${var_count},%(file_type)s" "${variant.input_variants}" "${variant.input_variants.ext}" "input_variants_${var_count}"
11 #end for 12 #end for
50 #for $pedigree_string in $gatk_param_type.pedigree_string_repeat: 51 #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
51 -p '--pedigreeString "${pedigree_string.pedigree_string}"' 52 -p '--pedigreeString "${pedigree_string.pedigree_string}"'
52 #end for 53 #end for
53 -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"' 54 -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
54 #for $read_filter in $gatk_param_type.read_filter: 55 #for $read_filter in $gatk_param_type.read_filter:
55 -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}" 56 -p '
57 #if ${read_filter.read_filter_type.read_filter_type_selector} not in $default_read_filters:
58 --read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
59 #end_if
56 ###raise Exception( str( dir( $read_filter ) ) ) 60 ###raise Exception( str( dir( $read_filter ) ) )
57 #for $name, $param in $read_filter.read_filter_type.iteritems(): 61 #for $name, $param in $read_filter.read_filter_type.iteritems():
58 #if $name not in [ "__current_case__", "read_filter_type_selector" ]: 62 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
59 #if hasattr( $param.input, 'truevalue' ): 63 #if hasattr( $param.input, 'truevalue' ):
60 ${param} 64 ${param}