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comparison tools/coverage_stats/coverage_stats.xml @ 1:d1fdfaae5dbe draft

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Uploaded v0.0.1b with warning about samtools 8000 coverage limit
author peterjc
date Fri, 21 Nov 2014 09:43:58 -0500
parents ca8f63f2f7d4
children 7254ece0c0ff
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0:ca8f63f2f7d4 1:d1fdfaae5dbe
73 73
74 In this example there were 604 contigs, each with one line in the output table, 74 In this example there were 604 contigs, each with one line in the output table,
75 plus the final row (labelled with an asterisk) representing 950320 unmapped reads. 75 plus the final row (labelled with an asterisk) representing 950320 unmapped reads.
76 In this BAM file, the fourth column was otherwise zero. 76 In this BAM file, the fourth column was otherwise zero.
77 77
78 .. class:: warningmark
79
80 **Note**. There is an internal hard limit of 8000 for the pileup routine in
81 samtools, meaning the reported coverage from ``samtools depth`` will show
82 maximum coverage depths *around* 8000.
83
78 84
79 **Citation** 85 **Citation**
80 86
81 If you use this Galaxy tool in work leading to a scientific publication please 87 If you use this Galaxy tool in work leading to a scientific publication please
82 cite: 88 cite: