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WGLab / doc-ANNOVAR

Documentation for the ANNOVAR software
http://annovar.openbioinformatics.org
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Getting zygosity (HOM or HET) in a column in txt output #72

Closed hamidqaedi closed 5 years ago

hamidqaedi commented 5 years ago

Hi Developers, Is there any method (code) to get variant zygosity into a column? I tried to find the solution with-withzyg option, but still lacking zygosity column in the final output. Any advice is greatly appreciated. Hamid

hamidqaedi commented 5 years ago

I figured it out using python and R. No I have such column in the annotation file. I suppose it should be incorporated into annotation file by default, as you may find in the output of other software like SnpEff. Hamid

kaichop commented 5 years ago

I missed this issue and did not respond earlier. -withzyg should print out the hom and het status. Then you annotate the file, and the additional column will be included in the final output (regardless of format), when -otherinfo argument is included in table_annovar.

On Mon, Oct 7, 2019 at 1:24 AM hamidqaedi notifications@github.com wrote:

I figured it out using python and R. No I have such column in the annotation file. I suppose it should be incorporated into annotation file by default, as you may find in the output of other software like SnpEff. Hamid

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