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changeset 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
files tools/coverage_stats/coverage_stats.xml
diffstat 1 files changed, 6 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- a/tools/coverage_stats/coverage_stats.xml	Fri Nov 21 09:28:29 2014 -0500
+++ b/tools/coverage_stats/coverage_stats.xml	Fri Nov 21 09:43:58 2014 -0500
@@ -75,6 +75,12 @@
 plus the final row (labelled with an asterisk) representing 950320 unmapped reads.
 In this BAM file, the fourth column was otherwise zero.
 
+.. class:: warningmark
+
+**Note**. There is an internal hard limit of 8000 for the pileup routine in
+samtools, meaning the reported coverage from ``samtools depth`` will show
+maximum coverage depths *around* 8000.
+
 
 **Citation**