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annotate tool-data/all_fasta.loc.sample @ 2:5d9c84514103 draft default tip

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit 7fe9d5207f75ba1d9632f2772dbb589b6aba937a"
author artbio
date Mon, 11 May 2020 04:18:20 -0400
parents 504de035ac0f
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
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1 #This file lists the locations and dbkeys of all the fasta files
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
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2 #under the "genome" directory (a directory that contains a directory
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
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3 #for each build). The script extract_fasta.py will generate the file
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
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4 #all_fasta.loc. This file has the format (white space characters are
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
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5 #TAB characters):
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
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6 #
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
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7 #<unique_build_id> <dbkey> <display_name> <file_path>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
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8 #
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
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9 #So, all_fasta.loc could look something like this:
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
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10 #
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
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13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
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14 #
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
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15 #Your all_fasta.loc file should contain an entry for each individual
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
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16 #fasta file. So there will be multiple fasta files for each build,
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
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17 #such as with hg19 above.
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
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18 #