Mercurial > repos > jjohnson > gatk2
changeset 35:a29c7d7d962d draft
Fix default read filter screening
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Fri, 01 Mar 2013 07:52:02 -0600 |
| parents | b99c25b0ad4d |
| children | 14d47237bb0a |
| files | base_recalibrator.xml depth_of_coverage.xml haplotype_caller.xml indel_realigner.xml print_reads.xml realigner_target_creator.xml reduce_reads.xml unified_genotyper.xml variant_annotator.xml variant_apply_recalibration.xml variant_combine.xml variant_eval.xml variant_filtration.xml variant_recalibrator.xml variant_select.xml variants_validate.xml |
| diffstat | 16 files changed, 54 insertions(+), 47 deletions(-) [+] |
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--- a/base_recalibrator.xml Thu Feb 28 15:41:24 2013 -0600 +++ b/base_recalibrator.xml Fri Mar 01 07:52:02 2013 -0600 @@ -61,8 +61,12 @@ -p '--pedigreeString "${pedigree_string.pedigree_string}"' #end for -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"' + #set default_read_filters = ['DuplicateRead','FailsVendorQualityCheck','NotPrimaryAlignment','MappingQualityZero','MalformedRead','MappingQualityUnavailable','UnmappedRead'] #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 $name not in [ "__current_case__", "read_filter_type_selector" ]: @@ -284,7 +288,7 @@ <!-- no extra options --> </when> <when value="MalformedRead"> - <!-- no extra options --> + <param name="filter_mismatching_base_and_quals" type="boolean" truevalue="--filter_mismatching_base_and_quals" falsevalue="" checked="false" label="filter out the reads with mismatching number of bases and base qualities" help="filter out the mismatch reads instead of quitting with an error"/> </when> <when value="MappingQuality"> <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
--- a/depth_of_coverage.xml Thu Feb 28 15:41:24 2013 -0600 +++ b/depth_of_coverage.xml Fri Mar 01 07:52:02 2013 -0600 @@ -48,10 +48,10 @@ -p '--pedigreeString "${pedigree_string.pedigree_string}"' #end for -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"' - #set default_read_filters = ['DuplicateReadFilter','FailsVendorQualityCheckFilter','NotPrimaryAlignmentFilter','MalformedReadFilter','UnmappedReadFilter'] + #set default_read_filters = ['DuplicateRead','FailsVendorQualityCheck','NotPrimaryAlignment','MalformedRead','UnmappedRead'] #for $read_filter in $gatk_param_type.read_filter: -p ' - #if ${read_filter.read_filter_type.read_filter_type_selector} not in $default_read_filters: + #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( $read_filter ) ) ) @@ -295,7 +295,7 @@ <!-- no extra options --> </when> <when value="MalformedRead"> - <!-- no extra options --> + <param name="filter_mismatching_base_and_quals" type="boolean" truevalue="--filter_mismatching_base_and_quals" falsevalue="" checked="false" label="filter out the reads with mismatching number of bases and base qualities" help="filter out the mismatch reads instead of quitting with an error"/> </when> <when value="MappingQuality"> <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
--- a/haplotype_caller.xml Thu Feb 28 15:41:24 2013 -0600 +++ b/haplotype_caller.xml Fri Mar 01 07:52:02 2013 -0600 @@ -36,8 +36,12 @@ -p '--pedigreeString "${pedigree_string.pedigree_string}"' #end for -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"' + #set default_read_filters = ['DuplicateRead','FailsVendorQualityCheck','NotPrimaryAlignment','MalformedRead','UnmappedRead'] #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 $name not in [ "__current_case__", "read_filter_type_selector" ]: @@ -273,7 +277,7 @@ <!-- no extra options --> </when> <when value="MalformedRead"> - <!-- no extra options --> + <param name="filter_mismatching_base_and_quals" type="boolean" truevalue="--filter_mismatching_base_and_quals" falsevalue="" checked="false" label="filter out the reads with mismatching number of bases and base qualities" help="filter out the mismatch reads instead of quitting with an error"/> </when> <when value="MappingQuality"> <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
--- a/indel_realigner.xml Thu Feb 28 15:41:24 2013 -0600 +++ b/indel_realigner.xml Fri Mar 01 07:52:02 2013 -0600 @@ -47,10 +47,10 @@ -p '--pedigreeString "${pedigree_string.pedigree_string}"' #end for -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"' - #set default_read_filters = ['MalformedReadFilter'] + #set default_read_filters = ['MalformedRead'] #for $read_filter in $gatk_param_type.read_filter: -p ' - #if ${read_filter.read_filter_type.read_filter_type_selector} not in $default_read_filters: + #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( $read_filter ) ) ) @@ -236,7 +236,7 @@ <!-- no extra options --> </when> <when value="MalformedRead"> - <!-- no extra options --> + <param name="filter_mismatching_base_and_quals" type="boolean" truevalue="--filter_mismatching_base_and_quals" falsevalue="" checked="false" label="filter out the reads with mismatching number of bases and base qualities" help="filter out the mismatch reads instead of quitting with an error"/> </when> <when value="MappingQuality"> <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
--- a/print_reads.xml Thu Feb 28 15:41:24 2013 -0600 +++ b/print_reads.xml Fri Mar 01 07:52:02 2013 -0600 @@ -37,10 +37,10 @@ -p '--pedigreeString "${pedigree_string.pedigree_string}"' #end for -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"' - #set default_read_filters = ['MalformedReadFilter'] + #set default_read_filters = ['MalformedRead'] #for $read_filter in $gatk_param_type.read_filter: -p ' - #if ${read_filter.read_filter_type.read_filter_type_selector} not in $default_read_filters: + #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 #for $name, $param in $read_filter.read_filter_type.iteritems(): @@ -216,7 +216,7 @@ <!-- no extra options --> </when> <when value="MalformedRead"> - <!-- no extra options --> + <param name="filter_mismatching_base_and_quals" type="boolean" truevalue="--filter_mismatching_base_and_quals" falsevalue="" checked="false" label="filter out the reads with mismatching number of bases and base qualities" help="filter out the mismatch reads instead of quitting with an error"/> </when> <when value="MappingQuality"> <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
--- a/realigner_target_creator.xml Thu Feb 28 15:41:24 2013 -0600 +++ b/realigner_target_creator.xml Fri Mar 01 07:52:02 2013 -0600 @@ -44,10 +44,10 @@ -p '--pedigreeString "${pedigree_string.pedigree_string}"' #end for -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"' - #set default_read_filters = ['DuplicateReadFilter','FailsVendorQualityCheckFilter','NotPrimaryAlignmentFilter','MappingQualityZeroFilter','MalformedReadFilter','BadCigarFilter','BadMateFilter','Platform454Filter','MappingQualityUnavailableFilter','UnmappedReadFilter'] + #set default_read_filters = ['DuplicateRead','FailsVendorQualityCheck','NotPrimaryAlignment','MappingQualityZero','MalformedRead','BadCigar','BadMate','Platform454','MappingQualityUnavailable','UnmappedRead'] #for $read_filter in $gatk_param_type.read_filter: -p ' - #if ${read_filter.read_filter_type.read_filter_type_selector} not in $default_read_filters: + #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 #for $name, $param in $read_filter.read_filter_type.iteritems(): @@ -221,7 +221,7 @@ <!-- no extra options --> </when> <when value="MalformedRead"> - <!-- no extra options --> + <param name="filter_mismatching_base_and_quals" type="boolean" truevalue="--filter_mismatching_base_and_quals" falsevalue="" checked="false" label="filter out the reads with mismatching number of bases and base qualities" help="filter out the mismatch reads instead of quitting with an error"/> </when> <when value="MappingQuality"> <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
--- a/reduce_reads.xml Thu Feb 28 15:41:24 2013 -0600 +++ b/reduce_reads.xml Fri Mar 01 07:52:02 2013 -0600 @@ -37,10 +37,10 @@ -p '--pedigreeString "${pedigree_string.pedigree_string}"' #end for -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"' - #set default_read_filters = ['MalformedReadFilter'] + #set default_read_filters = ['MalformedRead'] #for $read_filter in $gatk_param_type.read_filter: -p ' - #if ${read_filter.read_filter_type.read_filter_type_selector} not in $default_read_filters: + #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 #for $name, $param in $read_filter.read_filter_type.iteritems(): @@ -221,7 +221,7 @@ <!-- no extra options --> </when> <when value="MalformedRead"> - <!-- no extra options --> + <param name="filter_mismatching_base_and_quals" type="boolean" truevalue="--filter_mismatching_base_and_quals" falsevalue="" checked="false" label="filter out the reads with mismatching number of bases and base qualities" help="filter out the mismatch reads instead of quitting with an error"/> </when> <when value="MappingQuality"> <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
--- a/unified_genotyper.xml Thu Feb 28 15:41:24 2013 -0600 +++ b/unified_genotyper.xml Fri Mar 01 07:52:02 2013 -0600 @@ -5,7 +5,6 @@ <requirement type="package" version="0.1.18">samtools</requirement> </requirements> <command interpreter="python">gatk2_wrapper.py - #set default_read_filters = ['DuplicateReadFilter', 'FailsVendorQualityCheckFilter', 'NotPrimaryAlignmentFilter', 'MalformedReadFilter', 'BadMateFilter', 'MappingQualityUnavailableFilter', 'UnmappedReadFilter'] --max_jvm_heap_fraction "1" --stdout "${output_log}" #for $i, $input_bam in enumerate( $reference_source.input_bams ): @@ -52,10 +51,10 @@ -p '--pedigreeString "${pedigree_string.pedigree_string}"' #end for -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"' - #set default_read_filters = ['DuplicateReadFilter', 'FailsVendorQualityCheckFilter', 'NotPrimaryAlignmentFilter', 'MalformedReadFilter', 'BadMateFilter', 'MappingQualityUnavailableFilter', 'UnmappedReadFilter'] + #set default_read_filters = ['DuplicateRead', 'FailsVendorQualityCheck', 'NotPrimaryAlignment', 'MalformedRead', 'BadMate', 'MappingQualityUnavailable', 'UnmappedRead'] #for $read_filter in $gatk_param_type.read_filter: -p ' - #if ${read_filter.read_filter_type.read_filter_type_selector} not in $default_read_filters: + #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 #for $name, $param in $read_filter.read_filter_type.iteritems(): @@ -282,7 +281,7 @@ <!-- no extra options --> </when> <when value="MalformedRead"> - <!-- no extra options --> + <param name="filter_mismatching_base_and_quals" type="boolean" truevalue="--filter_mismatching_base_and_quals" falsevalue="" checked="false" label="filter out the reads with mismatching number of bases and base qualities" help="filter out the mismatch reads instead of quitting with an error"/> </when> <when value="MappingQuality"> <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
--- a/variant_annotator.xml Thu Feb 28 15:41:24 2013 -0600 +++ b/variant_annotator.xml Fri Mar 01 07:52:02 2013 -0600 @@ -82,10 +82,10 @@ -p '--pedigreeString "${pedigree_string.pedigree_string}"' #end for -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"' - #set default_read_filters = ['DuplicateReadFilter','FailsVendorQualityCheckFilter','NotPrimaryAlignmentFilter','MalformedReadFilter','UnmappedReadFilter'] + #set default_read_filters = ['DuplicateRead','FailsVendorQualityCheck','NotPrimaryAlignment','MalformedRead','UnmappedRead'] #for $read_filter in $gatk_param_type.read_filter: -p ' - #if ${read_filter.read_filter_type.read_filter_type_selector} not in $default_read_filters: + #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 #for $name, $param in $read_filter.read_filter_type.iteritems(): @@ -302,7 +302,7 @@ <!-- no extra options --> </when> <when value="MalformedRead"> - <!-- no extra options --> + <param name="filter_mismatching_base_and_quals" type="boolean" truevalue="--filter_mismatching_base_and_quals" falsevalue="" checked="false" label="filter out the reads with mismatching number of bases and base qualities" help="filter out the mismatch reads instead of quitting with an error"/> </when> <when value="MappingQuality"> <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
--- a/variant_apply_recalibration.xml Thu Feb 28 15:41:24 2013 -0600 +++ b/variant_apply_recalibration.xml Fri Mar 01 07:52:02 2013 -0600 @@ -33,10 +33,10 @@ -p '--pedigreeString "${pedigree_string.pedigree_string}"' #end for -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"' - #set default_read_filters = ['DuplicateReadFilter','FailsVendorQualityCheckFilter','NotPrimaryAlignmentFilter','MalformedReadFilter','UnmappedReadFilter'] + #set default_read_filters = ['DuplicateRead','FailsVendorQualityCheck','NotPrimaryAlignment','MalformedRead','UnmappedRead'] #for $read_filter in $gatk_param_type.read_filter: -p ' - #if ${read_filter.read_filter_type.read_filter_type_selector} not in $default_read_filters: + #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 #for $name, $param in $read_filter.read_filter_type.iteritems(): @@ -192,7 +192,7 @@ <!-- no extra options --> </when> <when value="MalformedRead"> - <!-- no extra options --> + <param name="filter_mismatching_base_and_quals" type="boolean" truevalue="--filter_mismatching_base_and_quals" falsevalue="" checked="false" label="filter out the reads with mismatching number of bases and base qualities" help="filter out the mismatch reads instead of quitting with an error"/> </when> <when value="MappingQuality"> <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
--- a/variant_combine.xml Thu Feb 28 15:41:24 2013 -0600 +++ b/variant_combine.xml Fri Mar 01 07:52:02 2013 -0600 @@ -39,10 +39,10 @@ -p '--pedigreeString "${pedigree_string.pedigree_string}"' #end for -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"' - #set default_read_filters = ['DuplicateReadFilter','FailsVendorQualityCheckFilter','NotPrimaryAlignmentFilter','MalformedReadFilter','UnmappedReadFilter'] + #set default_read_filters = ['DuplicateRead','FailsVendorQualityCheck','NotPrimaryAlignment','MalformedRead','UnmappedRead'] #for $read_filter in $gatk_param_type.read_filter: -p ' - #if ${read_filter.read_filter_type.read_filter_type_selector} not in $default_read_filters: + #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 #for $name, $param in $read_filter.read_filter_type.iteritems(): @@ -212,7 +212,7 @@ <!-- no extra options --> </when> <when value="MalformedRead"> - <!-- no extra options --> + <param name="filter_mismatching_base_and_quals" type="boolean" truevalue="--filter_mismatching_base_and_quals" falsevalue="" checked="false" label="filter out the reads with mismatching number of bases and base qualities" help="filter out the mismatch reads instead of quitting with an error"/> </when> <when value="MappingQuality"> <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
--- a/variant_eval.xml Thu Feb 28 15:41:24 2013 -0600 +++ b/variant_eval.xml Fri Mar 01 07:52:02 2013 -0600 @@ -47,10 +47,10 @@ -p '--pedigreeString "${pedigree_string.pedigree_string}"' #end for -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"' - #set default_read_filters = ['DuplicateReadFilter','FailsVendorQualityCheckFilter','NotPrimaryAlignmentFilter','MalformedReadFilter','UnmappedReadFilter'] + #set default_read_filters = ['DuplicateRead','FailsVendorQualityCheck','NotPrimaryAlignment','MalformedRead','UnmappedRead'] #for $read_filter in $gatk_param_type.read_filter: -p ' - #if ${read_filter.read_filter_type.read_filter_type_selector} not in $default_read_filters: + #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 #for $name, $param in $read_filter.read_filter_type.iteritems(): @@ -268,7 +268,7 @@ <!-- no extra options --> </when> <when value="MalformedRead"> - <!-- no extra options --> + <param name="filter_mismatching_base_and_quals" type="boolean" truevalue="--filter_mismatching_base_and_quals" falsevalue="" checked="false" label="filter out the reads with mismatching number of bases and base qualities" help="filter out the mismatch reads instead of quitting with an error"/> </when> <when value="MappingQuality"> <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
--- a/variant_filtration.xml Thu Feb 28 15:41:24 2013 -0600 +++ b/variant_filtration.xml Fri Mar 01 07:52:02 2013 -0600 @@ -43,10 +43,10 @@ -p '--pedigreeString "${pedigree_string.pedigree_string}"' #end for -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"' - #set default_read_filters = ['DuplicateReadFilter','FailsVendorQualityCheckFilter','NotPrimaryAlignmentFilter','MalformedReadFilter','UnmappedReadFilter'] + #set default_read_filters = ['DuplicateRead','FailsVendorQualityCheck','NotPrimaryAlignment','MalformedRead','UnmappedRead'] #for $read_filter in $gatk_param_type.read_filter: -p ' - #if ${read_filter.read_filter_type.read_filter_type_selector} not in $default_read_filters: + #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 #for $name, $param in $read_filter.read_filter_type.iteritems(): @@ -221,7 +221,7 @@ <!-- no extra options --> </when> <when value="MalformedRead"> - <!-- no extra options --> + <param name="filter_mismatching_base_and_quals" type="boolean" truevalue="--filter_mismatching_base_and_quals" falsevalue="" checked="false" label="filter out the reads with mismatching number of bases and base qualities" help="filter out the mismatch reads instead of quitting with an error"/> </when> <when value="MappingQuality"> <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
--- a/variant_recalibrator.xml Thu Feb 28 15:41:24 2013 -0600 +++ b/variant_recalibrator.xml Fri Mar 01 07:52:02 2013 -0600 @@ -51,10 +51,10 @@ -p '--pedigreeString "${pedigree_string.pedigree_string}"' #end for -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"' - #set default_read_filters = ['DuplicateReadFilter','FailsVendorQualityCheckFilter','NotPrimaryAlignmentFilter','MalformedReadFilter','UnmappedReadFilter'] + #set default_read_filters = ['DuplicateRead','FailsVendorQualityCheck','NotPrimaryAlignment','MalformedRead','UnmappedRead'] #for $read_filter in $gatk_param_type.read_filter: -p ' - #if ${read_filter.read_filter_type.read_filter_type_selector} not in $default_read_filters: + #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 #for $name, $param in $read_filter.read_filter_type.iteritems(): @@ -447,7 +447,7 @@ <!-- no extra options --> </when> <when value="MalformedRead"> - <!-- no extra options --> + <param name="filter_mismatching_base_and_quals" type="boolean" truevalue="--filter_mismatching_base_and_quals" falsevalue="" checked="false" label="filter out the reads with mismatching number of bases and base qualities" help="filter out the mismatch reads instead of quitting with an error"/> </when> <when value="MappingQuality"> <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
--- a/variant_select.xml Thu Feb 28 15:41:24 2013 -0600 +++ b/variant_select.xml Fri Mar 01 07:52:02 2013 -0600 @@ -103,10 +103,10 @@ -p '--pedigreeString "${pedigree_string.pedigree_string}"' #end for -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"' - #set default_read_filters = ['DuplicateReadFilter','FailsVendorQualityCheckFilter','NotPrimaryAlignmentFilter','MalformedReadFilter','UnmappedReadFilter'] + #set default_read_filters = ['DuplicateRead','FailsVendorQualityCheck','NotPrimaryAlignment','MalformedRead','UnmappedRead'] #for $read_filter in $gatk_param_type.read_filter: -p ' - #if ${read_filter.read_filter_type.read_filter_type_selector} not in $default_read_filters: + #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 #for $name, $param in $read_filter.read_filter_type.iteritems(): @@ -266,7 +266,7 @@ <!-- no extra options --> </when> <when value="MalformedRead"> - <!-- no extra options --> + <param name="filter_mismatching_base_and_quals" type="boolean" truevalue="--filter_mismatching_base_and_quals" falsevalue="" checked="false" label="filter out the reads with mismatching number of bases and base qualities" help="filter out the mismatch reads instead of quitting with an error"/> </when> <when value="MappingQuality"> <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
--- a/variants_validate.xml Thu Feb 28 15:41:24 2013 -0600 +++ b/variants_validate.xml Fri Mar 01 07:52:02 2013 -0600 @@ -36,10 +36,10 @@ -p '--pedigreeString "${pedigree_string.pedigree_string}"' #end for -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"' - #set default_read_filters = ['DuplicateReadFilter','FailsVendorQualityCheckFilter','NotPrimaryAlignmentFilter','MalformedReadFilter','UnmappedReadFilter'] + #set default_read_filters = ['DuplicateRead','FailsVendorQualityCheck','NotPrimaryAlignment','MalformedRead','UnmappedRead'] #for $read_filter in $gatk_param_type.read_filter: -p ' - #if ${read_filter.read_filter_type.read_filter_type_selector} not in $default_read_filters: + #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 #for $name, $param in $read_filter.read_filter_type.iteritems(): @@ -192,7 +192,7 @@ <!-- no extra options --> </when> <when value="MalformedRead"> - <!-- no extra options --> + <param name="filter_mismatching_base_and_quals" type="boolean" truevalue="--filter_mismatching_base_and_quals" falsevalue="" checked="false" label="filter out the reads with mismatching number of bases and base qualities" help="filter out the mismatch reads instead of quitting with an error"/> </when> <when value="MappingQuality"> <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>