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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