# HG changeset patch
# User wolma
# Date 1418509186 18000
# Node ID 099d2c4d800767d6553b1c2942635d3ec0888c7e
Imported from capsule None
diff -r 000000000000 -r 099d2c4d8007 bamsort.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bamsort.xml Sat Dec 13 17:19:46 2014 -0500
@@ -0,0 +1,38 @@
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+ Sort a BAM file by coordinates (or names) of the mapped reads
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+ mimodd
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+ mimodd version -q
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+ mimodd sort $inputfile -o $output --oformat $oformat $by_name
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+.. class:: infomark
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+ **What it does**
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+The tool sorts a BAM file of aligned reads, typically by the reference genome coordinates that the reads have been mapped to.
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+Coordinate-sorted input files are expected by most downstream MiModD tools, but note that the *SNAP Read Alignment* produces coordinate-sorted output by default and it is only necessary to sort files that come from other sources or from *SNAP Read Alignment* jobs with a custom sort order.
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+The option *Sort by read names instead of coordinates* is useful if you want to re-align coordinate-sorted paired-end data. In *paired-end mode*, the *SNAP Read Alignment* tool expects the reads in the input file to be arranged in read pairs, i.e., the forward read information of a pair must be followed immediately by its reverse mate information, which is typically not the case in coordinate-sorted files. Resorting such files by read names fixes this problem.
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diff -r 000000000000 -r 099d2c4d8007 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Sat Dec 13 17:19:46 2014 -0500
@@ -0,0 +1,6 @@
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