Re: Cannot invoke java.lang.CharSequence.length

[igv-help]

I would have to see the file, did you forget to attach it?

On Tuesday, January 9, 2024 at 9:58:35 AM UTC-8 MC wrote:

Hi everyone,

I'm currently inspecting some vcf files generated by Illumina sequencing, the GATK best practices workflow and Mutect2. When I try to open certain .vcf.gz files (one is attached) in IGV, I get this error message:

Error loading [file].Mutect.vcf.gz. Cannot invoke "java.lang.CharSequence.length()" because "this.text" is null.

I can open the other .vcf files normally and the file above was generated using identical methods to the other files. I have inspected the files after unzipping them and they seem to have the correct vcf structure.

Any ideas on how I could resolve this issue? Thanks!