From 62506054cd5df45826a39de31c98f14241ff1af7 Mon Sep 17 00:00:00 2001 From: Daniel Blankenberg Date: Tue, 10 Apr 2012 11:20:12 -0400 Subject: [PATCH] Add argument names to parameter help for GATK Advanced options. --- tools/gatk/count_covariates.xml | 312 +++++++++---------- tools/gatk/depth_of_coverage.xml | 336 ++++++++++----------- tools/gatk/indel_realigner.xml | 310 +++++++++---------- tools/gatk/print_reads.xml | 308 +++++++++---------- tools/gatk/realigner_target_creator.xml | 310 +++++++++---------- tools/gatk/table_recalibration.xml | 298 +++++++++--------- tools/gatk/unified_genotyper.xml | 320 ++++++++++---------- tools/gatk/variant_annotator.xml | 298 +++++++++--------- tools/gatk/variant_apply_recalibration.xml | 298 +++++++++--------- tools/gatk/variant_combine.xml | 298 +++++++++--------- tools/gatk/variant_eval.xml | 298 +++++++++--------- tools/gatk/variant_filtration.xml | 298 +++++++++--------- tools/gatk/variant_recalibrator.xml | 300 +++++++++--------- tools/gatk/variant_select.xml | 298 +++++++++--------- tools/gatk/variants_validate.xml | 298 +++++++++--------- 15 files changed, 2290 insertions(+), 2290 deletions(-) diff --git a/tools/gatk/count_covariates.xml b/tools/gatk/count_covariates.xml index c8df346894f..f3add3f8284 100644 --- a/tools/gatk/count_covariates.xml +++ b/tools/gatk/count_covariates.xml @@ -180,13 +180,13 @@ - - - - - - - + + + + + + + @@ -215,204 +215,204 @@ - - + + - - + + - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - + - + - + - - + + - - - - - - - - - - - - - + + + + + + + + + + + + + - - - - - - - - - - - - - + + + + + + + + + + + + + - + - - - - + + + + - + - + - - + + - - + + - - + + diff --git a/tools/gatk/depth_of_coverage.xml b/tools/gatk/depth_of_coverage.xml index 32da8d4f8ac..828a0df88aa 100644 --- a/tools/gatk/depth_of_coverage.xml +++ b/tools/gatk/depth_of_coverage.xml @@ -239,204 +239,204 @@ - - + + - - + + - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - + - + - + - - + + - - - - - - - - - - - - - + + + + + + + + + + + + + - - - - - - - - - - - - - + + + + + + + + + + + + + - + - - - - + + + + - + - + - - + + - - + + - - + + @@ -996,25 +996,25 @@ Go `here <http://www.broadinstitute.org/gsa/wiki/index.php/Input_files_for_th **Settings**:: - calculateCoverageOverGenes File NA Calculate the coverage statistics over this list of genes. Currently accepts RefSeq. - ignoreDeletionSites boolean false Ignore sites consisting only of deletions - includeDeletions boolean false Include information on deletions - maxBaseQuality byte 127 Maximum quality of bases to count towards depth. Defaults to 127 (Byte.MAX_VALUE). - maxMappingQuality int 2147483647 Maximum mapping quality of reads to count towards depth. Defaults to 2^31-1 (Integer.MAX_VALUE). - minBaseQuality byte -1 Minimum quality of bases to count towards depth. Defaults to -1. - minMappingQuality int -1 Minimum mapping quality of reads to count towards depth. Defaults to -1. - nBins int 499 Number of bins to use for granular binning - omitDepthOutputAtEachBase boolean false Will omit the output of the depth of coverage at each base, which should result in speedup - omitIntervalStatistics boolean false Will omit the per-interval statistics section, which should result in speedup - omitLocusTable boolean false Will not calculate the per-sample per-depth counts of loci, which should result in speedup - omitPerSampleStats boolean false Omits the summary files per-sample. These statistics are still calculated, so this argument will not improve runtime. - outputFormat String rtable the format of the output file (e.g. csv, table, rtable); defaults to r-readable table - partitionType Set[Partition] [sample] Partition type for depth of coverage. Defaults to sample. Can be any combination of sample, readgroup, library. - printBaseCounts boolean false Will add base counts to per-locus output. - printBinEndpointsAndExit boolean false Prints the bin values and exits immediately. Use to calibrate what bins you want before running on data. - start int 1 Starting (left endpoint) for granular binning - stop int 500 Ending (right endpoint) for granular binning - summaryCoverageThreshold int[] [15] for summary file outputs, report the % of bases coverd to >= this number. Defaults to 15; can take multiple arguments. + calculateCoverageOverGenes File NA Calculate the coverage statistics over this list of genes. Currently accepts RefSeq. + ignoreDeletionSites boolean false Ignore sites consisting only of deletions + includeDeletions boolean false Include information on deletions + maxBaseQuality byte 127 Maximum quality of bases to count towards depth. Defaults to 127 (Byte.MAX_VALUE). + maxMappingQuality int 2147483647 Maximum mapping quality of reads to count towards depth. Defaults to 2^31-1 (Integer.MAX_VALUE). + minBaseQuality byte -1 Minimum quality of bases to count towards depth. Defaults to -1. + minMappingQuality int -1 Minimum mapping quality of reads to count towards depth. Defaults to -1. + nBins int 499 Number of bins to use for granular binning + omitDepthOutputAtEachBase boolean false Will omit the output of the depth of coverage at each base, which should result in speedup + omitIntervalStatistics boolean false Will omit the per-interval statistics section, which should result in speedup + omitLocusTable boolean false Will not calculate the per-sample per-depth counts of loci, which should result in speedup + omitPerSampleStats boolean false Omits the summary files per-sample. These statistics are still calculated, so this argument will not improve runtime. + outputFormat String rtable the format of the output file (e.g. csv, table, rtable); defaults to r-readable table + partitionType Set[Partition] [sample] Partition type for depth of coverage. Defaults to sample. Can be any combination of sample, readgroup, library. + printBaseCounts boolean false Will add base counts to per-locus output. + printBinEndpointsAndExit boolean false Prints the bin values and exits immediately. Use to calibrate what bins you want before running on data. + start int 1 Starting (left endpoint) for granular binning + stop int 500 Ending (right endpoint) for granular binning + summaryCoverageThreshold int[] [15] for summary file outputs, report the % of bases coverd to >= this number. Defaults to 15; can take multiple arguments. ------ diff --git a/tools/gatk/indel_realigner.xml b/tools/gatk/indel_realigner.xml index 80fa4af1ee8..957dde797ee 100644 --- a/tools/gatk/indel_realigner.xml +++ b/tools/gatk/indel_realigner.xml @@ -146,12 +146,12 @@ - - - - - - + + + + + + @@ -179,204 +179,204 @@ - - + + - - + + - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - + - + - + - - + + - - - - - - - - - - - - - + + + + + + + + + + + + + - - - - - - - - - - - - - + + + + + + + + + + + + + - + - - - - + + + + - + - + - - + + - - + + - - + + diff --git a/tools/gatk/print_reads.xml b/tools/gatk/print_reads.xml index 5e0295430c1..51c1be0559b 100644 --- a/tools/gatk/print_reads.xml +++ b/tools/gatk/print_reads.xml @@ -147,204 +147,204 @@ - - + + - - + + - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - + - + - + - - + + - - - - - - - - - - - - - + + + + + + + + + + + + + - - - - - - - - - - - - - + + + + + + + + + + + + + - + - - - - + + + + - + - + - - + + - - + + - - + + @@ -407,11 +407,11 @@ Go `here <http://www.broadinstitute.org/gsa/wiki/index.php/Input_files_for_th **Settings**:: - number int -1 Print the first n reads from the file, discarding the rest - platform String NA Exclude all reads with this platform from the output - readGroup String NA Exclude all reads with this read group from the output - sample_file Set[File] [] File containing a list of samples (one per line). Can be specified multiple times - sample_name Set[String] [] Sample name to be included in the analysis. Can be specified multiple times. + number int -1 Print the first n reads from the file, discarding the rest + platform String NA Exclude all reads with this platform from the output + readGroup String NA Exclude all reads with this read group from the output + sample_file Set[File] [] File containing a list of samples (one per line). Can be specified multiple times + sample_name Set[String] [] Sample name to be included in the analysis. Can be specified multiple times. ------ diff --git a/tools/gatk/realigner_target_creator.xml b/tools/gatk/realigner_target_creator.xml index 3171ef42b38..a2ce3a0d24f 100644 --- a/tools/gatk/realigner_target_creator.xml +++ b/tools/gatk/realigner_target_creator.xml @@ -134,12 +134,12 @@ - - - - - - + + + + + + @@ -165,204 +165,204 @@ - - + + - - + + - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - + - + - + - - + + - - - - - - - - - - - - - + + + + + + + + + + + + + - - - - - - - - - - - - - + + + + + + + + + + + + + - + - - - - + + + + - + - + - - + + - - + + - - + + diff --git a/tools/gatk/table_recalibration.xml b/tools/gatk/table_recalibration.xml index 9ad3c451edc..46246074ec1 100644 --- a/tools/gatk/table_recalibration.xml +++ b/tools/gatk/table_recalibration.xml @@ -154,204 +154,204 @@ - - + + - - + + - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - + - + - + - - + + - - - - - - - - - - - - - + + + + + + + + + + + + + - - - - - - - - - - - - - + + + + + + + + + + + + + - + - - - - + + + + - + - + - - + + - - + + - - + + diff --git a/tools/gatk/unified_genotyper.xml b/tools/gatk/unified_genotyper.xml index de046faaccd..1847e3d72b5 100644 --- a/tools/gatk/unified_genotyper.xml +++ b/tools/gatk/unified_genotyper.xml @@ -179,12 +179,12 @@ - - - - - - + + + + + + @@ -220,204 +220,204 @@ - - + + - - + + - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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+ - + - + - + - - + + - - - - - - - - - - - - - + + + + + + + + + + + + + - - - - - - - - - - - - - + + + + + + + + + + + + + - + - - - - + + + + - + - + - - + + - - + + - - + + diff --git a/tools/gatk/variant_apply_recalibration.xml b/tools/gatk/variant_apply_recalibration.xml index 4fd2f13b84a..f2e19977209 100644 --- a/tools/gatk/variant_apply_recalibration.xml +++ b/tools/gatk/variant_apply_recalibration.xml @@ -135,204 +135,204 @@ - - + + - - + + - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - + - + - + - - + + - - - - - - - - - - - - - + + + + + + + + + + + + + - - - - - - - - - - - - - + + + + + + + + + + + + + - + - - - - + + + + - + - + - - + + - - + + - - + + diff --git a/tools/gatk/variant_combine.xml b/tools/gatk/variant_combine.xml index 456443ed295..20861fb9816 100644 --- a/tools/gatk/variant_combine.xml +++ b/tools/gatk/variant_combine.xml @@ -155,204 +155,204 @@ - - + + - - + + - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - + - + - + - - + + - - - - - - - - - - - - - + + + + + + + + + + + + + - - - - - - - - - - - - - + + + + + + + + + + + + + - + - - - - + + + + - + - + - - + + - - + + - - + + diff --git a/tools/gatk/variant_eval.xml b/tools/gatk/variant_eval.xml index c3dfec21c1d..73f739ba65b 100644 --- a/tools/gatk/variant_eval.xml +++ b/tools/gatk/variant_eval.xml @@ -211,204 +211,204 @@ - - + + - - + + - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - + - + - + - - + + - - - - - - - - - - - - - + + + + + + + + + + + + + - - - - - - - - - - - - - + + + + + + + + + + + + + - + - - - - + + + + - + - + - - + + - - + + - - + + diff --git a/tools/gatk/variant_filtration.xml b/tools/gatk/variant_filtration.xml index 5d3dd09df92..25e0b08ace4 100644 --- a/tools/gatk/variant_filtration.xml +++ b/tools/gatk/variant_filtration.xml @@ -164,204 +164,204 @@ - - + + - - + + - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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- + + - - + + - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - + - + - + - - + + - - - - - - - - - - - - - + + + + + + + + + + + + + - - - - - - - - - - - - - + + + + + + + + + + + + + - + - - - - + + + + - + - + - - + + - - + + - - + +