Notice:
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!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Attention:
We will be out of the office on October 14, 2019, due to the U.S. holiday. We will return to monitoring the forum on October 15.

GATK4 MergeVcfs / ValidateVariants does not support ambiguous (IUPAC) variants (b37 reference)

FPBarthelFPBarthel ✭✭HoustonMember ✭✭
edited July 2018 in Ask the GATK team

Perhaps this is intended, but GATK4 MergeVcfs / ValidateVariants do not support variants with ambiguous annotation, ie. 3:60830534-60830534 (M) in b37. ValidateVariants returns the following error when trying to validate a VCF file with such a base:

htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number n: unparsable vcf record with allele M

Best Answer

Answers

Sign In or Register to comment.