Assistance Needed: Exomiser Error - Fully-Closed Coordinates Out of Contig Bounds

[1995Q]

I am currently encountering an issue while using Exomiser for variant analysis, and I would greatly appreciate your expertise in resolving it. The specific error message I am encountering is as follows: "Fully-closed coordinates 3:198119972-198119972 out of contig bounds [1,198022430]"

From what I understand, this error indicates that the genomic coordinates specified in my VCF file fall outside the valid range for chromosome 3, which has a maximum length of 198022430 base pairs. Would you be able to provide guidance on how to address this issue?

[julesjacobsen]

Hi @1995Q

From what I understand, this error indicates that the genomic coordinates specified in my VCF file fall outside the valid range for chromosome 3, which has a maximum length of 198022430 base pairs.

This is correct. You should check that the input VCF was called against the same reference assembly as you state in the analysis.yaml

Your variant spans: 3:198119972-198119972

hg19 chromosome 3 length = 198022430 hg38 chromosome 3 length = 198295559

So this suggests your sample VCF was called against hg38 but you have set the assembly to for Exomiser to analyse it against to hg19.

In the analysis.yaml you're using as input for Exomiser:

    assembly: hg38 # set this to hg38