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annotate picard_EstimateLibraryComplexity.xml @ 3:52fdfc45590a draft

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author devteam
date Thu, 16 Jul 2015 15:32:31 -0400
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1 <tool name="EstimateLibraryComplexity" id="picard_EstimateLibraryComplexity" version="@TOOL_VERSION@.0">
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2 <description>assess sequence library complexity from read sequences</description>
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3 <macros>
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4 <import>picard_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command>
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8 @java_options@
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10 java -jar \$JAVA_JAR_PATH/picard.jar
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11 EstimateLibraryComplexity
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12
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13 INPUT="${inputFile}"
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14 OUTPUT="${outFile}"
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16 MIN_IDENTICAL_BASES="${min_identical_bases}"
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17 MAX_DIFF_RATE="${max_diff_rate}"
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18 MIN_MEAN_QUALITY="${min_mean_quality}"
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19 MAX_GROUP_RATIO="${max_group_ratio}"
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20 #import pipes
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21 READ_NAME_REGEX=${ pipes.quote( str( $read_name_regex ) ) or "''" }
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22 OPTICAL_DUPLICATE_PIXEL_DISTANCE="${optical_duplicate_pixel_distance}"
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23
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24 VALIDATION_STRINGENCY="${validation_stringency}"
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25 QUIET=true
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26 VERBOSITY=ERROR
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27
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28 </command>
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29 <inputs>
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30 <param format="bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" />
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31 <param name="min_identical_bases" type="integer" value="5" label="The minimum number of bases at the starts of reads that must be identical for reads to be grouped together for duplicate detection" help="MIN_IDENTICAL_BASES; In effect total_reads / 4^max_id_bases reads will be compared at a time, so lower numbers will produce more accurate results but consume exponentially more memory and CPU; default=5"/>
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32 <param name="max_diff_rate" type="float" value="0.03" label="The maximum rate of differences between two reads to call them identical" help="MAX_DIFF_RATE; default=0.03"/>
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33 <param name="min_mean_quality" type="integer" min="0" max="93" value="20" label="The minimum mean quality of the bases in a read pair for the read to be analyzed" help="MIN_MEAN_QUALITY; Reads with lower average quality are filtered out and not considered in any calculations; default=20"/>
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34 <param name="max_group_ratio" type="integer" value="500" label="Do not process self-similar groups that are this many times over the mean expected group size" help="MAX_GROUP_RATIO; I.e. if the input contains 10m read pairs and MIN_IDENTICAL_BASES is set to 5, then the mean expected group size would be approximately 10 reads; default-500"/>
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35
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36 <param name="read_name_regex" type="text" size="40" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*." label="Regular expression that can be used to parse read names in the incoming SAM/BAM dataset" help="READ_NAME_REGEX; Read names are parsed to extract three variables: tile/region, x coordinate and y coordinate. These values are used to estimate the rate of optical duplication in order to give a more accurate estimated library size. See help below for more info; default=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*.">
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37 <sanitizer>
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38 <valid initial="string.printable">
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39 </valid>
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40 </sanitizer>
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41 </param>
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42 <param name="optical_duplicate_pixel_distance" type="integer" value="100" min="0" max="500" label="The maximum offset between two duplicte clusters in order to consider them optical duplicates" help="OPTICAL_DUPLICATE_PIXEL_DISTANCE; default=100"/>
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43
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44 <expand macro="VS" />
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45
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46 </inputs>
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47
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48 <outputs>
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49 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Library complexity report"/>
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50 </outputs>
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51
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52 <tests>
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53 <test>
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54 <param name="inputFile" value="picard_EstimateLibraryComplexity.bam" ftype="bam"/>
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55 <param name="min_identical_bases" value="5"/>
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56 <param name="max_diff_rate" value="0.03"/>
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57 <param name="min_mean_quality" value="20"/>
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58 <param name="read_name_regex" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*."/>
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59 <param name="optical_duplicate_pixel_distance" value="100"/>
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60 <param name="max_group_ratio" value="500"/>
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61 <param name="validation_stringency" value="LENIENT"/>
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62 <output name="outFile" file="picard_EstimateLibraryComplexity_test1.tab" ftype="tabular" lines_diff="4"/>
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63 </test>
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64 </tests>
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65
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66 <stdio>
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67 <exit_code range="1:" level="fatal"/>
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68 </stdio>
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69
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70 <help>
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71
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72 **Purpose**
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73
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74 Attempts to estimate library complexity from sequence of read pairs alone. Does so by sorting all reads by the first N bases (5 by default)
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75 of each read and then comparing reads with the first N bases identical to each other for duplicates. Reads are considered to be duplicates
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76 if they match each other with no gaps and an overall mismatch rate less than or equal to MAX_DIFF_RATE (0.03 by default).
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77
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78 Reads of poor quality are filtered out so as to provide a more accurate estimate. The filtering removes reads with any no-calls in the first
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79 N bases or with a mean base quality lower than MIN_MEAN_QUALITY across either the first or second read.
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80
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81 Unpaired reads are ignored in this computation.
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82 The algorithm attempts to detect optical duplicates separately from PCR duplicates and excludes these in the calculation of library size.
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83
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84 Also, since there is no alignment to screen out technical reads one further filter is applied on the data. After examining all reads a Histogram
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85 is built of [#reads in duplicate set -> #of duplicate sets]; all bins that contain exactly one duplicate set are then removed from the Histogram
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86 as outliers before library size is estimated.
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87
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88 @dataset_collections@
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89
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90 @description@
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91
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92 MIN_IDENTICAL_BASES=Integer The minimum number of bases at the starts of reads that must be identical for reads to be
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93 grouped together for duplicate detection. In effect total_reads / 4^max_id_bases reads
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94 will be compared at a time, so lower numbers will produce more accurate results but
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95 consume exponentially more memory and CPU. Default value: 5.
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96
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97 MAX_DIFF_RATE=Double The maximum rate of differences between two reads to call them identical. Default value:
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98 0.03.
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99
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100 MIN_MEAN_QUALITY=Integer The minimum mean quality of the bases in a read pair for the read to be analyzed. Reads
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101 with lower average quality are filtered out and not considered in any calculations.
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102 Default value: 20.
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103
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104 MAX_GROUP_RATIO=Integer Do not process self-similar groups that are this many times over the mean expected group
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105 size. I.e. if the input contains 10m read pairs and MIN_IDENTICAL_BASES is set to 5, then
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106 the mean expected group size would be approximately 10 reads. Default value: 500.
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107
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108 READ_NAME_REGEX=String Regular expression that can be used to parse read names in the incoming SAM file. Read
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109 names are parsed to extract three variables: tile/region, x coordinate and y coordinate.
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110 These values are used to estimate the rate of optical duplication in order to give a more
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111 accurate estimated library size. Set this option to null to disable optical duplicate
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112 detection. The regular expression should contain three capture groups for the three
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113 variables, in order. It must match the entire read name. Note that if the default regex
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114 is specified, a regex match is not actually done, but instead the read name is split on
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115 colon character. For 5 element names, the 3rd, 4th and 5th elements are assumed to be
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116 tile, x and y values. For 7 element names (CASAVA 1.8), the 5th, 6th, and 7th elements
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117 are assumed to be tile, x and y values. Default value:
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118 [a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*.
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119
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120 OPTICAL_DUPLICATE_PIXEL_DISTANCE=Integer
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121 The maximum offset between two duplicte clusters in order to consider them optical
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122 duplicates. This should usually be set to some fairly small number (e.g. 5-10 pixels)
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123 unless using later versions of the Illumina pipeline that multiply pixel values by 10, in
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124 which case 50-100 is more normal. Default value: 100.
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125
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126
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127 @more_info@
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128
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129 </help>
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130 </tool>
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131
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132