# HG changeset patch # User devteam # Date 1392847278 18000 # Node ID fda8c17575854cc3472a39fe72875bc12d0aa3e4 # Parent 828b3e80f2503678ff7ae0aa6a3bf8b9c6ba5ef8 Uploaded diff -r 828b3e80f250 -r fda8c1757585 picard_SortSam.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/picard_SortSam.xml Wed Feb 19 17:01:18 2014 -0500 @@ -0,0 +1,50 @@ + + + + Sorts SAM or BAM file + picard + + picard_wrapper.py + --input "$inputFile" + -s "$sort_order" + -o "$outFile" + --output-format $outputFormat + -j "\$JAVA_JAR_PATH/SortSam.jar" + + + + + + + + + + + + + + + + + + +SortSam + +USAGE: SortSam [options] + +Documentation: http://picard.sourceforge.net/command-line-overview.shtml#SortSam + +Sorts the input SAM or BAM. + +Input and output formats are determined by file extension. +Option Description +INPUT=File The BAM or SAM file to sort. Required. +OUTPUT=File The sorted BAM or SAM output file. Required. +SORT_ORDER=SortOrder Sort order of output file Required. Possible values: {unsorted, queryname, coordinate} + + + + + +