# HG changeset patch # User wolma # Date 1418160410 18000 # Node ID 73644d9cb40afd435b22daa8073c20fbc9f76316 # Parent 074a654fd253377f05a432c4a2614acb3e928b30 version 0_1_5 diff -r 074a654fd253 -r 73644d9cb40a bamsort.xml --- a/bamsort.xml Wed Aug 13 07:14:20 2014 -0400 +++ b/bamsort.xml Tue Dec 09 16:26:50 2014 -0500 @@ -1,8 +1,9 @@ Sort a BAM file by coordinates (or names) of the mapped reads - mimodd + mimodd + mimodd version -q mimodd sort $inputfile -o $output --oformat $oformat $by_name @@ -28,9 +29,7 @@ The tool sorts a BAM file of aligned reads, typically by the reference genome coordinates that the reads have been mapped to. -Coordinate-sorted input files are expected by the downstream MiModD tools *Variant Calling and Coverage Analysis* and *Deletion prediction*. - -Note, however, 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. +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. 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.