Where do I gather indel and frameshift information in SnpEff output?

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6 weeks ago

mgranada3 ▴ 50

I performed WGWPS and used a GATK pipeline. The last step was to produce my SnpEff summary files but I am unsure where my indel and frameshift information is.

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My summary files appear to claim that all variants are SNPs.

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Do I need to perform a different analysis step in order to find my indels and frameshift changes?

frameshift WGWPS SnpEff GATK indels • 270 views

ADD COMMENT • link 5 weeks ago by mgranada3 ▴ 50

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ADD REPLY • link 6 weeks ago by Pierre Lindenbaum 164k

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Thanks for your help

ADD REPLY • link 5 weeks ago by mgranada3 ▴ 50

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