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annotate bwa_macros.xml @ 2:b4dfb5470bf3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 13b3ab10ff1a2e4be39b44f885df6bbe7c23099a
author devteam
date Fri, 30 Dec 2016 08:10:56 -0500
parents 8955a9521def
children b59a6178a6e0
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c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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1 <macros>
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2 <import>read_group_macros.xml</import>
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4 <token name="@VERSION@">0.7.15</token>
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c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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6 <token name="@set_rg_string@">
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7 #set $rg_string = "@RG\\tID:" + str($rg_id)
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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8 #set $rg_string += $format_read_group("\\tSM:", $rg_sm)
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9 #set $rg_string += $format_read_group("\\tPL:", $rg_pl)
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10 #set $rg_string += $format_read_group("\\tLB:", $rg_lb)
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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11 #set $rg_string += $format_read_group("\\tCN:", $rg_cn)
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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12 #set $rg_string += $format_read_group("\\tDS:", $rg_ds)
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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13 #set $rg_string += $format_read_group("\\tDT:", $rg_dt)
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14 #set $rg_string += $format_read_group("\\tFO:", $rg_fo)
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15 #set $rg_string += $format_read_group("\\tKS:", $rg_ks)
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16 #set $rg_string += $format_read_group("\\tPG:", $rg_pg)
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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17 #set $rg_string += $format_read_group("\\tPI:", $rg_pi)
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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18 #set $rg_string += $format_read_group("\\tPU:", $rg_pu)
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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19 </token>
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20
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21 <token name="@set_reference_fasta_filename@"><![CDATA[
b4dfb5470bf3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 13b3ab10ff1a2e4be39b44f885df6bbe7c23099a
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22 #if str( $reference_source.reference_source_selector ) == "history":
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23 #set $reference_fasta_filename = "localref.fa"
b4dfb5470bf3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 13b3ab10ff1a2e4be39b44f885df6bbe7c23099a
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24 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
b4dfb5470bf3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 13b3ab10ff1a2e4be39b44f885df6bbe7c23099a
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25 bwa index
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26 #if str($reference_source.index_a) != 'auto'
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27 -a ${reference_source.index_a}
b4dfb5470bf3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 13b3ab10ff1a2e4be39b44f885df6bbe7c23099a
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28 #end if
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29 "${reference_fasta_filename}" &&
b4dfb5470bf3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 13b3ab10ff1a2e4be39b44f885df6bbe7c23099a
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30 #else:
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31 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
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32 #end if
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33 ]]></token>
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34
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35 <xml name="requirements">
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36 <requirements>
2
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37 <requirement type="package" version="@VERSION@">bwa</requirement>
b4dfb5470bf3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 13b3ab10ff1a2e4be39b44f885df6bbe7c23099a
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38 <requirement type="package" version="1.3.1">samtools</requirement>
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c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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39 </requirements>
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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40 </xml>
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41
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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42 <xml name="stdio">
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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43 <stdio>
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44 <exit_code range="1:" />
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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45 <exit_code range=":-1" />
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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46 <regex match="Error:" />
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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47 <regex match="Exception:" />
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48 </stdio>
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49 </xml>
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50
2
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51 <macro name="reference_source_conditional">
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52 <conditional name="reference_source">
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53 <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below">
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54 <option value="cached">Use a built-in genome index</option>
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55 <option value="history">Use a genome from history and build index</option>
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56 </param>
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57 <when value="cached">
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58 <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
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59 <options from_data_table="bwa_mem_indexes">
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60 <filter type="sort_by" column="2" />
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61 <validator type="no_options" message="No indexes are available" />
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62 </options>
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63 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
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64 </param>
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65 </when>
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66 <when value="history">
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67 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="You can upload a FASTA sequence to the history and use it as reference" />
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68 <param name="index_a" type="select" label="Algorithm for constructing the BWT index" help="(-a)">
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69 <option value="auto">Auto. Let BWA decide the best algorithm to use</option>
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70 <option value="is">IS linear-time algorithm for constructing suffix array. It requires 5.37N memory where N is the size of the database. IS is moderately fast, but does not work with database larger than 2GB</option>
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71 <option value="bwtsw">BWT-SW algorithm. This method works also with big genomes</option>
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72 </param>
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73 </when>
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74 </conditional>
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75 </macro>
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76
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77 <macro name="dbKeyActionsBwa">
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78 <expand macro="dbKeyActions">
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79 <option type="from_data_table" name="bwa_indexes" column="1" offset="0">
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80 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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81 <filter type="param_value" ref="reference_source.ref_file" column="0"/>
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82 </option>
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83 </expand>
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84 </macro>
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85
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86 <macro name="dbKeyActionsBwaMem">
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87 <expand macro="dbKeyActions">
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88 <option type="from_data_table" name="bwa_mem_indexes" column="1" offset="0">
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89 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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90 <filter type="param_value" ref="reference_source.ref_file" column="0"/>
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91 </option>
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92 </expand>
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93 </macro>
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94
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95 <macro name="dbKeyActions">
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96 <actions>
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97 <conditional name="reference_source.reference_source_selector">
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98 <when value="cached">
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99 <action type="metadata" name="dbkey">
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100 <yield />
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101 </action>
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102 </when>
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103 <when value="history">
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104 <action type="metadata" name="dbkey">
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105 <option type="from_param" name="reference_source.ref_file" param_attribute="dbkey" />
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106 </action>
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107 </when>
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108 </conditional>
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109 </actions>
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110 </macro>
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111
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112 <token name="@RG@">
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113 -----
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114
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115 .. class:: warningmark
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116
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117 **Read Groups are Important!**
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118
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119 One of the recommended best practices in NGS analysis is adding read group information to BAM files. You can do this directly in BWA interface using the
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120 **Specify read group information?** widget. If you are not familiar with read groups you shold know that this is effectively a way to tag reads with an additional ID.
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121 This allows you to combine BAM files from, for example, multiple BWA runs into a single dataset. This significantly simplifies downstream processing as
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122 instead of dealing with multiple datasets you only have to handle only one. This is possible because the read group information allows you to identify
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123 data from different experiments even if they are combined in one file. Many downstream analysis tools such as varinat callers (e.g., FreeBayes or Naive Varinat Caller
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124 present in Galaxy) are aware of readgtroups and will automatically generate calls for each individual sample even if they are combined within a single file.
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125
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126 **Description of read groups fields**
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127
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128 (from GATK FAQ webpage):
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129
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130 .. csv-table::
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131 :header-rows: 1
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132
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133 Tag,Importance,Definition,Meaning
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134 "ID","Required","Read group identifier. Each @RG line must have a unique ID. The value of ID is used in the RG tags of alignment records. Must be unique among all read groups in header section. Read group IDs may be modified when merging SAM files in order to handle collisions.","Ideally, this should be a globally unique identify across all sequencing data in the world, such as the Illumina flowcell + lane name and number. Will be referenced by each read with the RG:Z field, allowing tools to determine the read group information associated with each read, including the sample from which the read came. Also, a read group is effectively treated as a separate run of the NGS instrument in tools like base quality score recalibration (a GATK component) -- all reads within a read group are assumed to come from the same instrument run and to therefore share the same error model."
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135 "SM","Sample. Use pool name where a pool is being sequenced.","Required. As important as ID.","The name of the sample sequenced in this read group. GATK tools treat all read groups with the same SM value as containing sequencing data for the same sample. Therefore it's critical that the SM field be correctly specified, especially when using multi-sample tools like the Unified Genotyper (a GATK component)."
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136 "PL","Platform/technology used to produce the read. Valid values: ILLUMINA, SOLID, LS454, HELICOS and PACBIO.","Important. Not currently used in the GATK, but was in the past, and may return. The only way to known the sequencing technology used to generate the sequencing data","It's a good idea to use this field."
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137 "LB","DNA preparation library identify","Essential for MarkDuplicates","MarkDuplicates uses the LB field to determine which read groups might contain molecular duplicates, in case the same DNA library was sequenced on multiple lanes."
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138
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139
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140 **Example of Read Group usage**
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141
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142 Suppose we have a trio of samples: MOM, DAD, and KID. Each has two DNA libraries prepared, one with 400 bp inserts and another with 200 bp inserts. Each of these libraries is run on two lanes of an illumina hiseq, requiring 3 x 2 x 2 = 12 lanes of data. When the data come off the sequencer, we would create 12 BAM files, with the following @RG fields in the header::
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143
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144 Dad's data:
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145 @RG ID:FLOWCELL1.LANE1 PL:illumina LB:LIB-DAD-1 SM:DAD PI:200
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146 @RG ID:FLOWCELL1.LANE2 PL:illumina LB:LIB-DAD-1 SM:DAD PI:200
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147 @RG ID:FLOWCELL1.LANE3 PL:illumina LB:LIB-DAD-2 SM:DAD PI:400
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148 @RG ID:FLOWCELL1.LANE4 PL:illumina LB:LIB-DAD-2 SM:DAD PI:400
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149
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150 Mom's data:
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151 @RG ID:FLOWCELL1.LANE5 PL:illumina LB:LIB-MOM-1 SM:MOM PI:200
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152 @RG ID:FLOWCELL1.LANE6 PL:illumina LB:LIB-MOM-1 SM:MOM PI:200
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153 @RG ID:FLOWCELL1.LANE7 PL:illumina LB:LIB-MOM-2 SM:MOM PI:400
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154 @RG ID:FLOWCELL1.LANE8 PL:illumina LB:LIB-MOM-2 SM:MOM PI:400
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155
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156 Kid's data:
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157 @RG ID:FLOWCELL2.LANE1 PL:illumina LB:LIB-KID-1 SM:KID PI:200
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158 @RG ID:FLOWCELL2.LANE2 PL:illumina LB:LIB-KID-1 SM:KID PI:200
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159 @RG ID:FLOWCELL2.LANE3 PL:illumina LB:LIB-KID-2 SM:KID PI:400
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160 @RG ID:FLOWCELL2.LANE4 PL:illumina LB:LIB-KID-2 SM:KID PI:400
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161
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162 Note the hierarchical relationship between read groups (unique for each lane) to libraries (sequenced on two lanes) and samples (across four lanes, two lanes for each library).
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163 </token>
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164 <token name="@info@">
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165 -----
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166
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167 .. class:: infomark
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168
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169 **More info**
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170
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171 To obtain more information about BWA and ask questions use these resources:
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172
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173 1. https://biostar.usegalaxy.org/
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174 2. https://www.biostars.org/
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175 3. https://github.com/lh3/bwa
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176 4. http://bio-bwa.sourceforge.net/
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177
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178 </token>
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179
0
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180 <token name="@dataset_collections@">
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181 ------
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182
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183 **Dataset collections - processing large numbers of datasets at once**
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184
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185 Dataset collections are in beta-testing. Extensive documentation will be added later this Spring.
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187
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188 </token>
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189
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190 </macros>