Snpefftomaf error: Changing the format column in vcf file
0
0
Entering edit mode
9 months ago
whb ▴ 20

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!

vcf maf snpeff snpefftomaf • 287 views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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!

ADD REPLY
0
Entering edit mode

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.

ADD REPLY

Login before adding your answer.

Traffic: 2700 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6