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1 <macros>
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2 <xml name="requirements">
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3 <requirements>
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4 <requirement type="package" version="1.2">samtools</requirement>
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5 <yield/>
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6 </requirements>
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7 </xml>
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8 <xml name="citations">
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9 <citations>
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10 <citation type="bibtex">
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11 @misc{SAM_def,
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12 title={Definition of SAM/BAM format},
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13 url = {https://samtools.github.io/hts-specs/SAMv1.pdf},}
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14 </citation>
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15 <citation type="doi">10.1093/bioinformatics/btp352</citation>
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16 <citation type="doi">10.1093/bioinformatics/btr076</citation>
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17 <citation type="doi">10.1093/bioinformatics/btr509</citation>
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18 <citation type="bibtex">
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19 @misc{Danecek_et_al,
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20 Author={Danecek, P., Schiffels, S., Durbin, R.},
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21 title={Multiallelic calling model in bcftools (-m)},
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22 url = {http://samtools.github.io/bcftools/call-m.pdf},}
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23 </citation>
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24 <citation type="bibtex">
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25 @misc{Durbin_VCQC,
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26 Author={Durbin, R.},
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27 title={Segregation based metric for variant call QC},
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28 url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},}
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29 </citation>
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30 <citation type="bibtex">
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31 @misc{Li_SamMath,
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32 Author={Li, H.},
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33 title={Mathematical Notes on SAMtools Algorithms},
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34 url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},}
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35 </citation>
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36 <citation type="bibtex">
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37 @misc{SamTools_github,
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38 title={SAMTools GitHub page},
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39 url = {https://github.com/samtools/samtools},}
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40 </citation>
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41 </citations>
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42 </xml>
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43 <xml name="version_command">
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44 <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command>
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45 </xml>
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46 <xml name="stdio">
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47 <stdio>
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48 <exit_code range="1:" level="fatal" description="Error" />
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49 </stdio>
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50 </xml>
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51 <token name="@no-chrom-options@">
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52 -----
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53
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54 .. class:: warningmark
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55
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56 **No options available? How to re-detect metadata**
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57
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58 If you see a "No options available" within the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop down, you need to re-detect metadata for the dataset you are trying to process. To do this follow these steps:
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59
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60 1. Click on the **pencil** icon adjacent to the dataset in the history
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61 2. A new menu will appear in the center pane of the interface
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62 3. Click **Datatype** tab
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63 4. Set **New Type** to **BAM**
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64 5. Click **Save**
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65
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66 The medatada will be re-detected and you will be able to see the list of reference sequences in the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop-down.
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67
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68 </token>
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69
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70 </macros>
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