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Question: Filtering for the frequency of ALT alleles
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gravatar for viviane.laine
4.0 years ago by
viviane.laine • 0
France
viviane.laine • 0 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 • 1.6k views
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modified 4.0 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.0 years ago by viviane.laine • 0
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gravatar for Jennifer Hillman Jackson
4.0 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 4.0 years ago by Jennifer Hillman Jackson ♦ 25k
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