Hello Matthew, The Galaxy wrapper for SAM-to-BAM takes as input a SAM file (sorted or unsorted) and produces a sorted BAM file, all in one step. Hopefully this helps, Best, Jen Galaxy team On 3/2/12 7:53 PM, Matthew McCormack wrote:
SAM-to-BAM (version 1.1.2) says that it produces an indexed BAM file based on a sorted input SAM file. When I go from SAM to BAM using SAMTools on my computer (not using Galaxy), I first convert the SAM to BAM then sort the BAM. I was wondering if on Galaxy you need to first sort the SAM file then use SAM-to-BAM to get the same result ?
Matthew
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