Mercurial > repos > sanbi-uwc > gatk2
annotate gatk2_picard_index.loc.sample @ 6:3a0582c3fb06 draft
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit 23bbc6e317e9979a1bade2af5d474f09fca3ff72
| author | sanbi-uwc |
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| date | Fri, 25 May 2018 07:35:20 -0400 |
| parents | 6e985e2e0802 |
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| rev | line source |
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6e985e2e0802
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204
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1 #This is a sample file distributed with Galaxy that enables tools |
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6e985e2e0802
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204
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2 #to use a directory of Picard dict and associated files. You will need |
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6e985e2e0802
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204
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3 #to create these data files and then create a picard_index.loc file |
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6e985e2e0802
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204
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4 #similar to this one (store it in this directory) that points to |
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6e985e2e0802
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204
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5 #the directories in which those files are stored. The picard_index.loc |
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6e985e2e0802
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204
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6 #file has this format (longer white space is the TAB character): |
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6e985e2e0802
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204
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7 # |
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6e985e2e0802
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204
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8 #<unique_build_id> <dbkey> <display_name> <fasta_file_path> |
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6e985e2e0802
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204
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9 # |
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6e985e2e0802
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204
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10 #So, for example, if you had hg18 indexed and stored in |
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6e985e2e0802
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204
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11 #/depot/data2/galaxy/srma/hg18/, |
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6e985e2e0802
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204
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12 #then the srma_index.loc entry would look like this: |
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6e985e2e0802
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204
sanbi-uwc
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13 # |
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6e985e2e0802
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204
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14 #hg18 hg18 hg18 Pretty /depot/data2/galaxy/picard/hg18/hg18.fa |
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6e985e2e0802
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204
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15 # |
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6e985e2e0802
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204
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16 #and your /depot/data2/galaxy/srma/hg18/ directory |
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6e985e2e0802
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204
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17 #would contain the following three files: |
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6e985e2e0802
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204
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18 #hg18.fa |
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6e985e2e0802
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204
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19 #hg18.dict |
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6e985e2e0802
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204
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20 #hg18.fa.fai |
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6e985e2e0802
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204
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21 # |
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6e985e2e0802
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204
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22 #The dictionary file for each reference (ex. hg18.dict) must be |
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6e985e2e0802
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204
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23 #created via Picard (http://picard.sourceforge.net). Note that |
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6e985e2e0802
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204
sanbi-uwc
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24 #the dict file does not have the .fa extension although the |
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6e985e2e0802
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204
sanbi-uwc
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25 #path list in the loc file does include it. |
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6e985e2e0802
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit f53888603dbab77d16c36cceffe0f2060052d204
sanbi-uwc
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26 # |