# HG changeset patch # User iuc # Date 1424277419 18000 # Node ID b80301676614271eccb92558ed5e3ea9110d1ee9 # Parent c2645201ffaec4b0544fddec9dc0890489667771 Uploaded diff -r c2645201ffae -r b80301676614 base_recalibrator.xml --- a/base_recalibrator.xml Tue Mar 11 07:42:09 2014 -0400 +++ b/base_recalibrator.xml Wed Feb 18 11:36:59 2015 -0500 @@ -1,6 +1,7 @@ - + calculates covariates used to recalibrate base quality scores of reads + gatk2_macros.xml @@ -302,4 +303,5 @@ @CITATION_SECTION@ + diff -r c2645201ffae -r b80301676614 depth_of_coverage.xml --- a/depth_of_coverage.xml Tue Mar 11 07:42:09 2014 -0400 +++ b/depth_of_coverage.xml Wed Feb 18 11:36:59 2015 -0500 @@ -1,6 +1,7 @@ - + on BAM files + gatk2_macros.xml @@ -692,7 +693,7 @@ DepthOfCoverage processes a set of bam files to determine coverage at different levels of partitioning and aggregation. Coverage can be analyzed per locus, per interval, per gene, or in total; can be partitioned by sample, by read group, by technology, by center, or by library; and can be summarized by mean, median, quartiles, and/or percentage of bases covered to or beyond a threshold. Additionally, reads and bases can be filtered by mapping or base quality score. -For more information on the GATK Depth of Coverage, see this `tool specific page <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_annotator_DepthOfCoverage.html>`_. +For more information on the GATK Depth of Coverage, see this `tool specific page <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_coverage_DepthOfCoverage.html>`_. To learn about best practices for variant detection using GATK, see this `overview <http://www.broadinstitute.org/gatk/guide/topic?name=best-practices>`_. @@ -738,4 +739,5 @@ @CITATION_SECTION@ + diff -r c2645201ffae -r b80301676614 gatk2_annotations.txt.sample --- a/gatk2_annotations.txt.sample Tue Mar 11 07:42:09 2014 -0400 +++ b/gatk2_annotations.txt.sample Wed Feb 18 11:36:59 2015 -0500 @@ -1,6 +1,5 @@ #unique_id name gatk_value tools_valid_for -#http://gatkforums.broadinstitute.org/discussion/1268/how-should-i-interpret-vcf-files-produced-by-the-gatk -AlleleBalance AlleleBalance AB UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller +AlleleBalance AlleleBalance AlleleBalance UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller AlleleBalanceBySample AlleleBalanceBySample AlleleBalanceBySample UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller BaseCounts BaseCounts BaseCounts UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller BaseQualityRankSumTest BaseQualityRankSumTest BaseQualityRankSumTest UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller @@ -13,7 +12,6 @@ HardyWeinberg HardyWeinberg HardyWeinberg UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller HomopolymerRun HomopolymerRun HomopolymerRun UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller InbreedingCoeff InbreedingCoeff InbreedingCoeff UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller -IndelType IndelType IndelType UnifiedGenotyper,VariantAnnotator,VariantRecalibrator LowMQ LowMQ LowMQ UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller MVLikelihoodRatio MVLikelihoodRatio MVLikelihoodRatio VariantAnnotator,VariantRecalibrator,HaplotypeCaller MappingQualityRankSumTest MappingQualityRankSumTest MappingQualityRankSumTest UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller @@ -26,20 +24,3 @@ SampleList SampleList SampleList UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller SnpEff SnpEff SnpEff VariantAnnotator,VariantRecalibrator,HaplotypeCaller SpanningDeletions SpanningDeletions SpanningDeletions UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller -VariantType VariantType VariantType UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller -AlleleCount Allele count in genotypes, for each ALT allele (AC) AC UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller -AlleleFrequency Allele Frequency, for each ALT allele (AF) AF UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller -AlleleNumber Total number of alleles in called genotypes (AN) AN UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller -Coverage Unfiltered depth over all samples (DP) DP UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller -Dels Dels Dels UnifiedGenotyper,VariantAnnotator,VariantRecalibrator -MQ RMS Mapping Quality MQ UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller -MQ0 Mapping Quality Zero MQ0 UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller -BaseQualityRankSumTest BaseQualityRankSumTest BaseQualityRankSumTest UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller -MappingQualityRankSumTest MappingQualityRankSumTest MappingQualityRankSumTest UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller -ReadPosRankSumTest ReadPosRankSumTest ReadPosRankSumTest UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller -HaplotypeScore HaplotypeScore HaplotypeScore UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller -QualByDepth QualByDepth QD UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller -VQSLOD Variant quality score recalibration VQSLOD UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller -FisherStrand FisherStrand FS UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller -StrandBias Strand Bias evidence (higher SB, more bias, more false positive calls) SB UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller - diff -r c2645201ffae -r b80301676614 gatk2_macros.xml --- a/gatk2_macros.xml Tue Mar 11 07:42:09 2014 -0400 +++ b/gatk2_macros.xml Wed Feb 18 11:36:59 2015 -0500 @@ -6,11 +6,16 @@ picard GATK2_PATH GATK2_SITE_OPTIONS + + + java -jar "$GATK2_PATH/GenomeAnalysisTK.jar" --help|grep '^The Genome' + --num_threads \${GALAXY_SLOTS:-4} + 2.8 java -jar "\$GATK2_PATH/GenomeAnalysisTK.jar" @@ -55,7 +60,7 @@ #end for -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"' - + -p '--interval_padding "${gatk_param_type.interval_padding}"' -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"' #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE": -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"' @@ -218,7 +223,9 @@ - + + @@ -296,7 +303,7 @@ - + @@ -318,6 +325,12 @@ + + + + + @@ -342,4 +355,11 @@ If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* + + + 10.1038/ng.806 + 10.1101/gr.107524.110 + 10.1002/0471250953.bi1110s43 + + diff -r c2645201ffae -r b80301676614 haplotype_caller.xml --- a/haplotype_caller.xml Tue Mar 11 07:42:09 2014 -0400 +++ b/haplotype_caller.xml Wed Feb 18 11:36:59 2015 -0500 @@ -1,6 +1,7 @@ - + Call SNPs and indels simultaneously via local de-novo assembly of haplotypes in an active region + gatk2_macros.xml @@ -30,6 +31,7 @@ #end if ' @DBSNP_OPTIONS@ + $allow_n_cigar_reads #include source=$standard_gatk_options# ##start analysis specific options @@ -138,7 +140,8 @@ - + + @@ -320,4 +323,5 @@ @CITATION_SECTION@ + diff -r c2645201ffae -r b80301676614 indel_realigner.xml --- a/indel_realigner.xml Tue Mar 11 07:42:09 2014 -0400 +++ b/indel_realigner.xml Wed Feb 18 11:36:59 2015 -0500 @@ -1,6 +1,7 @@ - + - perform local realignment + gatk2_macros.xml @@ -38,7 +39,8 @@ #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1 -d "-known:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}" #end for - + + $allow_n_cigar_reads #include source=$standard_gatk_options# ##start analysis specific options -d "-targetIntervals" "${target_intervals}" "${target_intervals.ext}" "gatk_target_intervals" @@ -110,7 +112,8 @@ - + + @@ -206,4 +209,5 @@ @CITATION_SECTION@ + diff -r c2645201ffae -r b80301676614 print_reads.xml --- a/print_reads.xml Tue Mar 11 07:42:09 2014 -0400 +++ b/print_reads.xml Wed Feb 18 11:36:59 2015 -0500 @@ -1,6 +1,7 @@ - + on BAM files + gatk2_macros.xml @@ -32,11 +33,6 @@ #include source=$standard_gatk_options# - #if str( $reference_source.reference_source_selector ) == "history": - -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input" - #end if - ##end standard gatk options - ##start analysis specific options #if $analysis_param_type.analysis_param_type_selector == "advanced": -p ' @@ -202,7 +198,7 @@ This walker is designed to work as the second pass in a two-pass processing step, doing a by-read traversal. For each base in each read this walker calculates various user-specified covariates (such as read group, reported quality score, cycle, and dinuc) Using these values as a key in a large hashmap the walker calculates an empirical base quality score and overwrites the quality score currently in the read. This walker then outputs a new bam file with these updated (recalibrated) reads. Note: This walker expects as input the recalibration table file generated previously by CovariateCounterWalker. Note: This walker is designed to be used in conjunction with CovariateCounterWalker. -For more information on base quality score recalibration using the GATK, see this `tool specific page <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_PrintReads.html>`_. +For more information on base quality score recalibration using the GATK, see this `tool specific page <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_readutils_PrintReads.html>`_. To learn about best practices for variant detection using GATK, see this `overview <http://www.broadinstitute.org/gatk/guide/topic?name=best-practices>`_. @@ -247,4 +243,5 @@ @CITATION_SECTION@ + diff -r c2645201ffae -r b80301676614 readme.rst --- a/readme.rst Tue Mar 11 07:42:09 2014 -0400 +++ b/readme.rst Wed Feb 18 11:36:59 2015 -0500 @@ -63,7 +63,8 @@ History ======= -v0.1 - Initial public release +* v0.1 - Initial public release +* v2.8.0 - Bugfix release, increase version number to reflect the underlying GATK version Licence (MIT) diff -r c2645201ffae -r b80301676614 realigner_target_creator.xml --- a/realigner_target_creator.xml Tue Mar 11 07:42:09 2014 -0400 +++ b/realigner_target_creator.xml Wed Feb 18 11:36:59 2015 -0500 @@ -1,6 +1,7 @@ - + for use in local realignment + gatk2_macros.xml @@ -37,7 +38,8 @@ #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1 -d "-known:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}" #end for - + + $allow_n_cigar_reads #include source=$standard_gatk_options# ##start analysis specific options #if $analysis_param_type.analysis_param_type_selector == "advanced": @@ -97,13 +99,17 @@ - + + - + - - - + + + @@ -164,4 +170,5 @@ @CITATION_SECTION@ + diff -r c2645201ffae -r b80301676614 reduce_reads.xml --- a/reduce_reads.xml Tue Mar 11 07:42:09 2014 -0400 +++ b/reduce_reads.xml Wed Feb 18 11:36:59 2015 -0500 @@ -1,6 +1,7 @@ - + in BAM files + gatk2_macros.xml @@ -154,7 +155,7 @@ This walker will generated reduced versions of the BAM files that still follow the BAM spec and contain all the information necessary for the GSA variant calling pipeline. Some options allow you to tune in how much compression you want to achieve. The default values have been shown to reduce a typical whole exome BAM file 100x. The higher the coverage, the bigger the savings in file size and performance of the downstream tools. -For more information on using read based compression in the GATK, see this `tool specific page <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_compression_reducereads_ReduceReads.html>`_. +.. For more information on using read based compression in the GATK, see this `tool specific page <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_compression_reducereads_ReduceReads.html>`_. To learn about best practices for variant detection using GATK, see this `overview <http://www.broadinstitute.org/gatk/guide/topic?name=best-practices>`_. @@ -223,4 +224,5 @@ @CITATION_SECTION@ + diff -r c2645201ffae -r b80301676614 test-data/phiX.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phiX.fasta Wed Feb 18 11:36:59 2015 -0500 @@ -0,0 +1,79 @@ +>phiX174 +GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT +GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA +ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG +TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA +GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC +TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT +TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT +CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT +TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG +TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC +GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA +CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAG +TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT +AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC +CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA +TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC +TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA +CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA +GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT +GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA +ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC +TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT +TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC +ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCGTGATGTTATTTCTTCATTTGGAGGTAAAAC +CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT +GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC +CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC +TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG +TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT +TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA +AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT +TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT +ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC +GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC +TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT +TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA +TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG +TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC +CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG +AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC +CGGGCAATAATGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT +TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG +CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA +AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT +GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG +GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA +TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT +CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG +TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA +GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC +CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA +TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA +AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC +TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT +CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA +TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG +TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT +CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT +TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC +ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG +TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA +ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG +GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC +CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT +GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGATGAATGCAATGCGACAG +GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT +ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG +CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC +CGTCTTCATTTCCATGCGGTGCATTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC +GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT +CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG +CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA +TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT +TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG +TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC +AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC +TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA + diff -r c2645201ffae -r b80301676614 tool_dependencies.xml --- a/tool_dependencies.xml Tue Mar 11 07:42:09 2014 -0400 +++ b/tool_dependencies.xml Wed Feb 18 11:36:59 2015 -0500 @@ -15,38 +15,12 @@ - + - + - - - - - - - - - - https://github.com/bgruening/download_store/raw/master/gatk2_R_deps/colorspace_1.2-4.tar.gz - https://github.com/bgruening/download_store/raw/master/gatk2_R_deps/stringr_0.6.2.tar.gz - https://github.com/bgruening/download_store/raw/master/gatk2_R_deps/RColorBrewer_1.0-5.tar.gz - https://github.com/bgruening/download_store/raw/master/gatk2_R_deps/dichromat_2.0-0.tar.gz - https://github.com/bgruening/download_store/raw/master/gatk2_R_deps/munsell_0.4.2.tar.gz - https://github.com/bgruening/download_store/raw/master/gatk2_R_deps/labeling_0.2.tar.gz - https://github.com/bgruening/download_store/raw/master/gatk2_R_deps/plyr_1.8.1.tar.gz - https://github.com/bgruening/download_store/raw/master/gatk2_R_deps/digest_0.6.4.tar.gz - https://github.com/bgruening/download_store/raw/master/gatk2_R_deps/gtable_0.1.2.tar.gz - https://github.com/bgruening/download_store/raw/master/gatk2_R_deps/reshape2_1.2.2.tar.gz - https://github.com/bgruening/download_store/raw/master/gatk2_R_deps/scales_0.2.3.tar.gz - https://github.com/bgruening/download_store/raw/master/gatk2_R_deps/proto_0.3-10.tar.gz - https://github.com/bgruening/download_store/raw/master/gatk2_R_deps/ggplot2_0.9.3.1.tar.gz - - - - - R depencies for GATK2. - + + diff -r c2645201ffae -r b80301676614 unified_genotyper.xml --- a/unified_genotyper.xml Tue Mar 11 07:42:09 2014 -0400 +++ b/unified_genotyper.xml Wed Feb 18 11:36:59 2015 -0500 @@ -1,6 +1,7 @@ - + SNP and indel caller + gatk2_macros.xml @@ -32,7 +33,7 @@ --standard_min_confidence_threshold_for_emitting "${standard_min_confidence_threshold_for_emitting}" ' @DBSNP_OPTIONS@ - + $allow_n_cigar_reads #include source=$standard_gatk_options# ##start analysis specific options #if $analysis_param_type.analysis_param_type_selector == "advanced": @@ -72,7 +73,6 @@ --excludeAnnotation "${annotation}" #end for #end if - ${analysis_param_type.multiallelic} #if str( $analysis_param_type.sample_ploidy ) != '': --sample_ploidy "$analysis_param_type.sample_ploidy" #end if @@ -121,12 +121,14 @@ - + - - + + @@ -192,14 +194,16 @@ - + - + @@ -294,4 +298,5 @@ @CITATION_SECTION@ + diff -r c2645201ffae -r b80301676614 variant_annotator.xml --- a/variant_annotator.xml Tue Mar 11 07:42:09 2014 -0400 +++ b/variant_annotator.xml Wed Feb 18 11:36:59 2015 -0500 @@ -1,6 +1,7 @@ - + + gatk2_macros.xml @@ -244,4 +245,5 @@ @CITATION_SECTION@ + diff -r c2645201ffae -r b80301676614 variant_apply_recalibration.xml --- a/variant_apply_recalibration.xml Tue Mar 11 07:42:09 2014 -0400 +++ b/variant_apply_recalibration.xml Wed Feb 18 11:36:59 2015 -0500 @@ -1,6 +1,7 @@ - + + gatk2_macros.xml @@ -135,4 +136,5 @@ @CITATION_SECTION@ + diff -r c2645201ffae -r b80301676614 variant_combine.xml --- a/variant_combine.xml Tue Mar 11 07:42:09 2014 -0400 +++ b/variant_combine.xml Wed Feb 18 11:36:59 2015 -0500 @@ -1,6 +1,7 @@ - + + gatk2_macros.xml @@ -167,4 +168,5 @@ @CITATION_SECTION@ + diff -r c2645201ffae -r b80301676614 variant_eval.xml --- a/variant_eval.xml Tue Mar 11 07:42:09 2014 -0400 +++ b/variant_eval.xml Wed Feb 18 11:36:59 2015 -0500 @@ -1,6 +1,7 @@ - + + gatk2_macros.xml @@ -80,10 +81,6 @@ --minPhaseQuality "${analysis_param_type.min_phase_quality}" - #if str( $analysis_param_type.family ): - --family_structure "${analysis_param_type.family}" - #end if - --mendelianViolationQualThreshold "${analysis_param_type.mendelian_violation_qual_threshold}" #if str( $analysis_param_type.ancestral_alignments ) != "None": @@ -165,9 +162,8 @@ - + diff -r c2645201ffae -r b80301676614 variant_filtration.xml --- a/variant_filtration.xml Tue Mar 11 07:42:09 2014 -0400 +++ b/variant_filtration.xml Wed Feb 18 11:36:59 2015 -0500 @@ -1,6 +1,7 @@ - + on VCF files + gatk2_macros.xml @@ -177,4 +178,5 @@ @CITATION_SECTION@ + diff -r c2645201ffae -r b80301676614 variant_recalibrator.xml --- a/variant_recalibrator.xml Tue Mar 11 07:42:09 2014 -0400 +++ b/variant_recalibrator.xml Wed Feb 18 11:36:59 2015 -0500 @@ -1,6 +1,9 @@ - + - + + ggplot2 + + gatk2_macros.xml @@ -110,7 +113,7 @@ - + @@ -329,8 +332,7 @@ - - + @@ -399,8 +401,7 @@ shrinkage The shrinkage parameter in variational Bayes algorithm. dirichlet The dirichlet parameter in variational Bayes algorithm. priorCounts The number of prior counts to use in variational Bayes algorithm. - percentBadVariants What percentage of the worst scoring variants to use when building the Gaussian mixture model of bad variants. 0.07 means bottom 7 percent. - minNumBadVariants The minimum amount of worst scoring variants to use when building the Gaussian mixture model of bad variants. Will override -percentBad arugment if necessary. + minNumBadVariants The minimum amount of worst scoring variants to use when building the Gaussian mixture model of bad variants. recal_file The output recal file used by ApplyRecalibration target_titv The expected novel Ti/Tv ratio to use when calculating FDR tranches and for display on optimization curve output figures. (approx 2.15 for whole genome experiments). ONLY USED FOR PLOTTING PURPOSES! TStranche The levels of novel false discovery rate (FDR, implied by ti/tv) at which to slice the data. (in percent, that is 1.0 for 1 percent) @@ -411,4 +412,5 @@ @CITATION_SECTION@ + diff -r c2645201ffae -r b80301676614 variant_select.xml --- a/variant_select.xml Tue Mar 11 07:42:09 2014 -0400 +++ b/variant_select.xml Wed Feb 18 11:36:59 2015 -0500 @@ -1,6 +1,7 @@ - + from VCF files + gatk2_macros.xml @@ -285,4 +286,5 @@ @CITATION_SECTION@ + diff -r c2645201ffae -r b80301676614 variant_validate.xml --- a/variant_validate.xml Tue Mar 11 07:42:09 2014 -0400 +++ b/variant_validate.xml Wed Feb 18 11:36:59 2015 -0500 @@ -1,6 +1,7 @@ - + + gatk2_macros.xml @@ -101,4 +102,5 @@ @CITATION_SECTION@ +