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If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
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Unparsable vcf record with allele *

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
Best Answer
-
- 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)
Answers
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.
What I did eventually was to remove all the multi-allelic sites using bcftools view -m2 -M2 -v snps file.vcf.gz
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.
@Michele I had that error message recently because I'd missed a new-line backslash. GATK tolerates 0/* but other programs don't.
@Michele @Will_Gilks
Hi,
What exactly was the error message you get with SelectVariants and what was the exact command you ran?
Thanks,
Sheila