Coordinate sorted sam

[prepagam]

I need to create a galaxy only pipeline for a course which trims, aligns then calls variants in GaTK.
I aligned with BWA, but cannot proceed further as the sam file is coordinate unsorted (SO:unsorted)
Sortsam is not available in Galaxy. I have tried various things like Picard reorder Sam and Bam, but it is still unsorted by coordinate. I also tried Paired Read Mate Fixer also from Picard, which has a sort order option. The out file states SO:coordinate, but looking at it - it is ordered chr1, chr10, chr11, chr12, chr13 …. chr2, chr21……

Does anyone know what else I might try?

[dpryan]

chr1, chr10, chr11 is properly coordinate sorted (chr10 comes before chr2, alphabetically). If you're interested in using GATK, what you need to ensure is that your BAM files and reference annotation have the same sort order.