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annotate bwa_macros.xml @ 1:8955a9521def draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
author devteam
date Fri, 18 Dec 2015 18:51:08 -0500
parents c9c78719ef26
children b4dfb5470bf3
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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>
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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2 <import>read_group_macros.xml</import>
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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3 <token name="@set_rg_string@">
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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4 #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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5 #set $rg_string += $format_read_group("\\tSM:", $rg_sm)
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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6 #set $rg_string += $format_read_group("\\tPL:", $rg_pl)
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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7 #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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8 #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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9 #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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10 #set $rg_string += $format_read_group("\\tDT:", $rg_dt)
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("\\tFO:", $rg_fo)
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("\\tKS:", $rg_ks)
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("\\tPG:", $rg_pg)
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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14 #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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15 #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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16 </token>
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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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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18 <xml name="requirements">
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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19 <requirements>
1
8955a9521def planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
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20 <requirement type="package" version="0.7.12">bwa</requirement>
0
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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21 <requirement type="package" version="1.2">samtools</requirement>
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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22 </requirements>
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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23 </xml>
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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24
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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25 <xml name="stdio">
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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26 <stdio>
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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27 <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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28 <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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29 <regex match="Error:" />
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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30 <regex match="Exception:" />
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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31 </stdio>
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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32 </xml>
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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33
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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34 <macro name="dbKeyActionsBwa">
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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35 <expand macro="dbKeyActions">
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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36 <option type="from_data_table" name="bwa_indexes" column="1" offset="0">
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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37 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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38 <filter type="param_value" ref="reference_source.ref_file" column="0"/>
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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39 </option>
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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40 </expand>
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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41 </macro>
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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42
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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43 <macro name="dbKeyActionsBwaMem">
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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44 <expand macro="dbKeyActions">
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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45 <option type="from_data_table" name="bwa_mem_indexes" column="1" offset="0">
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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46 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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47 <filter type="param_value" ref="reference_source.ref_file" column="0"/>
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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48 </option>
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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49 </expand>
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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50 </macro>
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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51
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52 <macro name="dbKeyActions">
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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53 <actions>
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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54 <conditional name="reference_source.reference_source_selector">
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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55 <when value="cached">
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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56 <action type="metadata" name="dbkey">
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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57 <yield />
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58 </action>
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59 </when>
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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60 <when value="history">
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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61 <action type="metadata" name="dbkey">
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62 <option type="from_param" name="reference_source.ref_file" param_attribute="dbkey" />
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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63 </action>
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64 </when>
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65 </conditional>
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66 </actions>
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67 </macro>
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68
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69 <token name="@RG@">
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70 -----
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71
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72 .. class:: warningmark
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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73
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74 **Read Groups are Important!**
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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75
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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76 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
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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77 **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.
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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78 This allows you to combine BAM files from, for example, multiple BWA runs into a single dataset. This significantly simplifies downstream processing as
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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79 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
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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80 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
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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81 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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83 **Description of read groups fields**
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85 (from GATK FAQ webpage):
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86
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87 .. csv-table::
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88 :header-rows: 1
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89
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90 Tag,Importance,Definition,Meaning
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91 "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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92 "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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93 "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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94 "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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95
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96
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97 **Example of Read Group usage**
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98
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99 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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100
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101 Dad's data:
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102 @RG ID:FLOWCELL1.LANE1 PL:illumina LB:LIB-DAD-1 SM:DAD PI:200
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103 @RG ID:FLOWCELL1.LANE2 PL:illumina LB:LIB-DAD-1 SM:DAD PI:200
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104 @RG ID:FLOWCELL1.LANE3 PL:illumina LB:LIB-DAD-2 SM:DAD PI:400
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105 @RG ID:FLOWCELL1.LANE4 PL:illumina LB:LIB-DAD-2 SM:DAD PI:400
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106
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107 Mom's data:
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108 @RG ID:FLOWCELL1.LANE5 PL:illumina LB:LIB-MOM-1 SM:MOM PI:200
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109 @RG ID:FLOWCELL1.LANE6 PL:illumina LB:LIB-MOM-1 SM:MOM PI:200
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110 @RG ID:FLOWCELL1.LANE7 PL:illumina LB:LIB-MOM-2 SM:MOM PI:400
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111 @RG ID:FLOWCELL1.LANE8 PL:illumina LB:LIB-MOM-2 SM:MOM PI:400
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112
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113 Kid's data:
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114 @RG ID:FLOWCELL2.LANE1 PL:illumina LB:LIB-KID-1 SM:KID PI:200
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115 @RG ID:FLOWCELL2.LANE2 PL:illumina LB:LIB-KID-1 SM:KID PI:200
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116 @RG ID:FLOWCELL2.LANE3 PL:illumina LB:LIB-KID-2 SM:KID PI:400
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117 @RG ID:FLOWCELL2.LANE4 PL:illumina LB:LIB-KID-2 SM:KID PI:400
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118
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119 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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120 </token>
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121 <token name="@info@">
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122 -----
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123
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124 .. class:: infomark
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125
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126 **More info**
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127
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128 To obtain more information about BWA and ask questions use these resources:
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129
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130 1. https://biostar.usegalaxy.org/
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131 2. https://www.biostars.org/
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132 3. https://github.com/lh3/bwa
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133 4. http://bio-bwa.sourceforge.net/
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134
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135 </token>
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136
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137 <token name="@dataset_collections@">
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138 ------
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139
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140 **Dataset collections - processing large numbers of datasets at once**
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141
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142 Dataset collections are in beta-testing. Extensive documentation will be added later this Spring.
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143
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144
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145 </token>
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146
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147 </macros>