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Update tool_dependencies
author Jim Johnson <jj@umn.edu>
date Tue, 11 Mar 2014 08:22:41 -0500
parents f2e4e81f3639
children
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1 **What it does**
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3 This tool uses the samtools view command in SAMTools toolkit to filter a SAM or BAM file on the MAPQ (mapping quality), FLAG bits, Read Group, Library, or region.
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5 **Input**
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7 Input is either a SAM or BAM file.
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9 **Output**
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11 The output file will be of the same format a the Input file, filtered by the selected options.
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13 **Options**
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15 Filtering by read group or library requires headers in the input SAM or BAM file.
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17 If regions are specified, only alignments overlapping the specified regions will be output. An alignment may be given multiple times if it is overlapping several regions.
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18 A region can be presented, for example, in the following format
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20 chr2 (the whole chr2)
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21 chr2:1000000 (region starting from 1,000,000bp)
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22 chr2:1,000,000-2,000,000 (region between 1,000,000 and 2,000,000bp including the end points).
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24 Note: The coordinate is 1-based.
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26 Multiple regions may be specified, separated by a space character
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28 chr2:1000000-2000000 chr2:1,000,000-2,000,000 chrX
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