Snpefftomaf error: Changing the format column in vcf file

Question

[whb]

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 https://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!

[Pierre Lindenbaum]

looks like you have a multiallelic VCF. Try to use bcftools norm to fix.

[whb]

Thank you for the reply. May I ask how do you know it is a multi allelic VCF? Does multiallelic VCF indicates something is wrong? Just want to learn so I know next time. and usually what would cause this?Any chance skipping the CalculateContamination and LearnReadOrientationModel steps can lead to this? because these are the steps I skipped.... thanks again!

[Pierre Lindenbaum]

May I ask how do you know it is a multi allelic VCF

1255,0 looks like a pattern of data when there is more than one ALT allele. It is just my hypothesis.