I have a question about the NGS: Indel Analysis toolset in 
Galaxy.  I have aligned my samples from Illumina's HiSeq2000 to the reference 
genome using BWA.  I've called SNPs using SAMTools and now need to call indels. 
 Under the NGS: Indel Analysis toolset, I see two options: "Filter Indels for 
SAM" and "Extract indels from SAM."  Since the descriptions are a little vague, 
I would presume that I start with the "Filter Indels for SAM" first on the BWA 
SAM file and then run "Extract indels from SAM" on the "Filter" output SAM file 
(i.e. BWA SAM -> Filter Indels for SAM -> Extract indels from SAM).  Is this 
the correct order?  Or would I skip the "Filter Indels for SAM" step (since the 
BWA SAM file technically already contains indels so there would be no need to 
filter) and just go straight to "Extract indels from SAM" (i.e. BWA SAM -> 
Extract indels from SAM)?
                I've tried both ways and get different results.  For example:

1.       BWA SAM -> Filter Indels for SAM -> Extract indels from SAM -> gives 
me 26,417 regions of interest

2.       BWA SAM -> Extract indels from SAM -> gives me 93,974 regions of 

                Which way is correct?  Any help/info would be greatly 


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