Question: Filtering for the frequency of ALT alleles
gravatar for viviane.laine
4.0 years ago by
viviane.laine0 wrote:


When running CloudMap unmapped mutant workflow, I get a SnpEff file with Homozygous or heterozygous status for each called variant. However I would like to have the ratio of alternate non-reference alleles / total number of alleles, to set up the threshold as I would like. Then:

-Would it be possible to have the ratio of ALT / TOT for each variant instead of « homozygous » or « heterozygous » in the homozygous field of the tabular file?

-If not, is it possible to filter the data in VCF file before running the SnpEff tool? Which expression should I use?


snpeff vcf filter • 1.6k views
ADD COMMENTlink modified 4.0 years ago by Jennifer Hillman Jackson25k • written 4.0 years ago by viviane.laine0
gravatar for Jennifer Hillman Jackson
4.0 years ago by
United States
Jennifer Hillman Jackson25k wrote:


You might like these tools, found in the group "NGS: Variant Analysis" on the public Main Galaxy site at (and also the Tool Shed, if working elsewhere Usage instructions are on the tool forms. 


Or possibly -

Naive Variant Caller
followed by Variant Annotator

Thanks, Jen, Galaxy team

ADD COMMENTlink written 4.0 years ago by Jennifer Hillman Jackson25k
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