Unparsable vcf record with allele *

lawal · January 2016

Hi guys,
I have recently jointly called 27 full genome data using GenotypeGVCFs approach. While i was trying to extract some chromosomes from the final file, i got this error
The provided VCF file is malformed at approximately line number 16076: Unparsable vcf record with allele *.

I look into the file and I found some of the multi-allellic sites having * as seen in the attached picture.

I feel the problem could be that the program realised that more than one allele is present at that position but could not ascertain which allele. I may be wrong but please what do you think I can do to solve this problem.
LAWAL

Redmar_van_den_Berg · January 2016

means that the snip in that sample is missing due to an overlapping deletion. (e.g sample 1 has a deletion of 10bp at position 1, and then sample 2 has a snip at position 3. In that case, the allele for sample 1 at position 3 would be *). This is allowed in the vcf standard, so you should probably contact the authors of the program that gives you that error. (See the vcf standard for details)

Redmar_van_den_Berg · January 2016

means that the snip in that sample is missing due to an overlapping deletion. (e.g sample 1 has a deletion of 10bp at position 1, and then sample 2 has a snip at position 3. In that case, the allele for sample 1 at position 3 would be *). This is allowed in the vcf standard, so you should probably contact the authors of the program that gives you that error. (See the vcf standard for details)

lawal · January 2016

Thank you Redmar_van_den_Berg. I have read the manual and contacted the authors. The moment i get a solution, I will post it here for future benefit.

lawal · January 2016

What I did eventually was to remove all the multi-allelic sites using bcftools view -m2 -M2 -v snps file.vcf.gz

Michele · March 2016

I have the same error in the same variant calling scenario using the SelectVariants tool. I also am interested in the resolution to this error.

Will_Gilks · March 2016

@Michele I had that error message recently because I'd missed a new-line backslash. GATK tolerates 0/* but other programs don't.

Sheila · March 2016

@Michele @Will_Gilks
Hi,

What exactly was the error message you get with SelectVariants and what was the exact command you ran?

Thanks,
Sheila

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Unparsable vcf record with allele *

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