Question: multiple data SnpEff variant effect and annotation
gravatar for ninakmrajala
9 months ago by
ninakmrajala10 wrote:

I am trying to do snpEFF variant effect and annotation on multiple data sets - however I always get a message: Please verify this parameter. Sequence changes (SNPs, MNPs, InDels)

I am not sure what this means and why I can´t carry on with the analysis

variant snp annotation snpeff • 338 views
ADD COMMENTlink modified 9 months ago by Jennifer Hillman Jackson25k • written 9 months ago by ninakmrajala10
gravatar for Jennifer Hillman Jackson
9 months ago by
United States
Jennifer Hillman Jackson25k wrote:


The first option Sequence changes (SNPs, MNPs, InDels) on the SnpEff tool is where the VCF input dataset is selected.

The second option on the tool form Input format is where VCF datatype is specified.

Note: BEDdata can be input instead of VCF, and selected as the input format, but annotating BED datasets is a deprecated function (as noted in the second option's choices) and might now work as expected.

The message you report is tool form help to alert about mismatches in the inputs/parameters before a job is submitted. To avoid this, check to see if you have one type of input selected for the first option and if the datatype is a mismatch for the second option. The input dataset (VCF or BED) should have that datatype assigned and be a match for the datatype specification.

Thanks! Jen, Galaxy

ADD COMMENTlink modified 9 months ago • written 9 months ago by Jennifer Hillman Jackson25k
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