Question: Filtering for the frequency of ALT alleles
0
gravatar for viviane.laine
3.3 years ago by
France
viviane.laine0 wrote:

Hi,

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?

Thanks!

snpeff vcf filter • 1.3k views
ADD COMMENTlink modified 3.3 years ago by Jennifer Hillman Jackson24k • written 3.3 years ago by viviane.laine0
0
gravatar for Jennifer Hillman Jackson
3.3 years ago by
United States
Jennifer Hillman Jackson24k wrote:

Hello,

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

Annotate

Or possibly -

Naive Variant Caller
followed by Variant Annotator

Thanks, Jen, Galaxy team

ADD COMMENTlink written 3.3 years ago by Jennifer Hillman Jackson24k
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