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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