allele ID out of range

[Marta Baragli]

Hi,

I am trying to use rtg vcfeval to benchmark different variant callers for SNV and Indels. However I keep getting this error:

"Error: VCF record GT contains allele ID out of range". 

The VCF record is:

chr3      155616677       .       AGGGGACAGAGAAGAGACAGATTCAGCTGGCCTCAAACTGTCTTTATTGGGTCTTGTTATTTGGAAAGCTGTCTCCTCTCTATAAAATAATAAAGGATTTTTGCTTTTTTGAAATCTTTGAGTTAATCACTTTG  .       22.03   PASS    .       GT:GQ:PS   1|0:2.27:155412822 

I believe the problem is that the alternative allele is "." instead of a nucleotide sequence but I'm not sure and I don't know how to solve that. 

Do you know if that might actually be the issue and how could I fix my VCF records?

Thank you

Marta.

[Sean Irvine]

Hi Marta,

You are correct, the problem is that the record is referring to an alternate (ALT) allele which does not exist in the record. In fact, the record is not valid VCF. Clearly, vcfeval cannot evaluate the correctness of the call if the bases of the actual bases of the call are missing.  You will need to look earlier in your pipeline to discover where / what tool is introducing this error.

Sean.

--
You received this message because you are subscribed to the Google Groups "RTG Users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to rtg-users+...@realtimegenomics.com.
To view this discussion on the web visit https://groups.google.com/a/realtimegenomics.com/d/msgid/rtg-users/637b7af9-9bbc-4bd0-961a-29ff50940f06n%40realtimegenomics.com.