Question: Ngs: Indel Analysis Tool Order
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David K Crossman • 130 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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modified 7.3 years ago
by
Jennifer Hillman Jackson ♦ 25k
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written
7.3 years ago by
David K Crossman • 130
