Maj/Min vs Ref/Alt - Can I make sure my VCF comes out of production with Ref/Alt instead of Maj/Min coded?

[Zachary Winn]

Hi TASSEL Team!

I know that this question has been asked before (https://groups.google.com/g/tassel/c/olBzvxcEIZk/m/KVCMIDfeAgAJ?pli=1), but I am currently working with multiple VCFs, and I need a TASSEL generated GBS VCF that is coded as Ref/Alt rather than Maj/Min. I read through that conversation, but I did not find an answer to my posed question.

Essentially, the header of my VCF generated by TASSEL say the following:

##Tassel=<ID=GenotypeTable,Version=5,Description="Reference allele is not known. The major allele was used as reference allele">

But I need to make sure that my produced VCF is in Ref/Alt instead of Maj/Min. Is there any way for TASSEL to produce a VCF which is informed by reference instead of major minor?

Thanks,

Zachary Winn, PhD

Postdoctoral Research Scholar 

USDA-ARS Eastern Regional Small Grains Genotyping Lab

[Zachary Winn]

Hi again,

I have done a little digging in the documentation for the ProductionSNPCallerPluginV2 for flags in the standalone pipeline. It appears there is no flag to provide a reference genome when calling... Does this mean that the VCF will always be put out as Major/Minor alleles instead of Reference/Alternative when referencing a .db file produced by TASSEL?

Thanks,

Zach

[Lynn Carol Johnson]

Yes, that is correct.  You will get Major/Minor vs Ref/Alt when referencing the .db created by the GBS pipeline.

We are not currently doing updates to the GBSv2 pipeline.  However, the code is open source and we welcome others to supply updates if they choose.

 

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[Zachary Winn]

Good to know. Thank you, Lynn. I will look for alternative solutions to my issue. You may now close the issue!

Have a good day,

Zach

[Zachary Winn]

Just as a minor update to this issue for people reading this in the future...

I wrote a little program in Bash to handle this issue. Essentially, it references the positions given in a VCF to a reference genome sequence (in this case I was using IWGSC RefSeqv2.1) and it uses those positions to check each SNP listed in a VCF. If the "reference allele" given for the position in the VCF does not match the reference genome provided, the program will attempt to correct the VCFs ref/alt to match the reference genome sequence. You can pull the program from my github here.

Thanks,

Zach

[Lynn Carol Johnson]

Zachary – thank you for sharing this!

 

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