Error with bayesTyperTools combine

[stephaniemyan]

Hi,

I'm trying to use bayesTyperTools combine to combine two VCF files. When I run the program, I get this error message:

[14/02/2019 15:29:52] You are using BayesTyperTools (v1.4)

[14/02/2019 15:29:52] Running BayesTyperTools (v1.4) combine on 2 files ...

bayesTyperTools: /isdata/kroghgrp/jasi/bayesTyper/code/releases/v1.4_static/BayesTyper-1.4/src/vcf++/Allele.cpp:63: Allele::Allele(const string&): Assertion `_seq.find_first_not_of("ACGTRYSWKMBDHVN") == string::npos' failed.
Aborted

Here's the command I'm using:

bayesTyperTools combine -v sgdp:sgdp_snvs.vcf.gz,gorilla:gorilla_snvs.vcf.gz -o combined.vcf.gz -z

And here are the first 1000 lines of the VCFs for reference: sgdp_snvs_1000.vcf.zip gorilla_snvs_1000.vcf.zip

I'm not sure what's off about the VCF files. Could you tell me what the error message means and how to go about debugging it?

Thanks, Steph

[jonassibbesen]

Hi Steph,

Thank you for writing. This error occurs when either the reference or the alternative allele contains characters that are not part of the IUPAC nucleotide code. I looked through the gorilla vcf you provided and found multiple lines where the alternative allele is missing ('.' character is used):

chr1    904283  .   C   .   96.23   PASS
chr1    904436  .   T   .   2916.03 PASS

BayesTyper does not support sites without an alternative allele. Therefore, try to remove them and run combine again.

Let me know if it does not work.

Best,

Jonas

[stephaniemyan]

Hi Jonas,

Thank you for your prompt response. Removing the '.' alts fixed this error, but now I have a new one:

[15/02/2019 10:12:12] You are using BayesTyperTools (v1.4)

[15/02/2019 10:12:12] Running BayesTyperTools (v1.4) combine on 2 files ...

bayesTyperTools: /isdata/kroghgrp/jasi/bayesTyper/code/releases/v1.4_static/BayesTyper-1.4/src/vcf++/VcfMetaData.cpp:55: uint VcfMetaData::numColumns() const: Assertion `header_added' failed.
Aborted

It looks like it might be an issue with the header now? Do you know how I could fix this one?

Thanks, Steph

[jonassibbesen]

Glad it worked. The new error occurs when the #CHROM row in the header is missing or not correctly formatted. Would it be possible to upload the vcf like before?

Thanks,

Jonas