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Hello,

The "Filter Indels" tool is intended to act as a quality screen before "Extract Indels" is used. Whether you want to use this step is something you will need to determine, as are the exact criteria for filtering. The best advice is to examine a sample of the differences between the two methods and tune or exclude the Filter step.

Hopefully this helps,

Best,

Jen
Galaxy team


On 8/22/11 11:58 AM, David K Crossman wrote:
Hello!

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 interest

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

Thanks,

David



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___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
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