Mercurial > repos > wolma > mimodd_bamsort
changeset 1:73644d9cb40a draft
version 0_1_5
| author | wolma |
|---|---|
| date | Tue, 09 Dec 2014 16:26:50 -0500 |
| parents | 074a654fd253 |
| children | 31e73b5e7278 |
| files | bamsort.xml |
| diffstat | 1 files changed, 3 insertions(+), 4 deletions(-) [+] |
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--- 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 @@ <tool id="bamsort" name="Sort BAM file"> <description>Sort a BAM file by coordinates (or names) of the mapped reads</description> <requirements> - <requirement type="package" version="0.1.3">mimodd</requirement> + <requirement type="package" version="0.1.5">mimodd</requirement> </requirements> + <version_command>mimodd version -q</version_command> <command> mimodd sort $inputfile -o $output --oformat $oformat $by_name </command> @@ -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.