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.

When I call Indels from my vcf file using GATK analysis tools I ger an Error!

Hi I used the GATK pipeline until I got a vcf that had SNPs and Indels, so I used GATK Analysis tools to remove SNPs and keep Indels. But after adding the reference genome, dictionary and index I get this error:

The provided VCF file is malformed at approximately line number 455: Unparsable vcf record with allele *, for input source: /home/helenadarmancier/Documents/Estagio/Original/vcf_NoAngH201_NoMono.vcf

How can I fix this?



Sign In or Register to comment.