gravatar for Ash

2 hours ago by

Hi I have a vcf file from Mutect2. I have annotated it with snpEff and want to convert it to MAF using snpefftomaf.pl but I keep getting this kind error:

Argument "1255,0" isn't numeric in numeric lt
Use of uninitialized value $minAF in numeric
Use of uninitialized value $minDP in numeric

They suggest changing the format from GT:AD:AF:DP:F1R2:F2R1:SBto GT:AD:DP will solve this error
github.com/tsy19900929/snpeffToMaf/blob/master/issues.png

But how can I do this? Is there any tools to change the format or did I miss something while variant call using Mutect2?

Thanks!

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modified 2 hours ago

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2 hours ago
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Ash10



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