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annotate tool-data/sam_fa_indices.loc.sample @ 8:d5f866df45ae

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author blankenberg
date Thu, 29 Jan 2015 15:02:01 -0500
parents ae6edc0012ba
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ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
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1 #This is a sample file distributed with Galaxy that enables tools
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
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2 #to use a directory of Samtools indexed sequences data files. You will need
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
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3 #to create these data files and then create a sam_fa_indices.loc file
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
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4 #similar to this one (store it in this directory) that points to
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
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5 #the directories in which those files are stored. The sam_fa_indices.loc
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
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6 #file has this format (white space characters are TAB characters):
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
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7 #
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
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8 #index <seq> <location>
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Daniel Blankenberg <dan@bx.psu.edu>
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9 #
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
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10 #So, for example, if you had hg18 indexed stored in
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
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11 #/depot/data2/galaxy/sam/,
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
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12 #then the sam_fa_indices.loc entry would look like this:
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
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13 #
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
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14 #index hg18 /depot/data2/galaxy/sam/hg18.fa
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
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15 #
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
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16 #and your /depot/data2/galaxy/sam/ directory
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
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17 #would contain hg18.fa and hg18.fa.fai files:
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
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18 #
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Daniel Blankenberg <dan@bx.psu.edu>
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19 #-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.fa
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
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20 #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.fa.fai
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
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21 #
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
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22 #Your sam_fa_indices.loc file should include an entry per line for
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
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23 #each index set you have stored. The file in the path does actually
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
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24 #exist, but it should never be directly used. Instead, the name serves
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
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25 #as a prefix for the index file. For example:
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
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26 #
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
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27 #index hg18 /depot/data2/galaxy/sam/hg18.fa
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Daniel Blankenberg <dan@bx.psu.edu>
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28 #index hg19 /depot/data2/galaxy/sam/hg19.fa