hello,
when running the varType command, I came across some strange behavior:
variants that have an "empty" ALT field (i.e. ".") are annotated with an info field called "INTERVAL", but this field is not added as a header to the vcf file. This of course causes issues in further steps of the pipeline.
Is this a known issue? am I possibly doing something wrong? I tried searching the documentation but "INTERVAL" is not one of the expected varType options
Thank you in advance,
Talya Dor (bioinformatician, Illumina)
hello, when running the varType command, I came across some strange behavior: variants that have an "empty" ALT field (i.e. ".") are annotated with an info field called "INTERVAL", but this field is not added as a header to the vcf file. This of course causes issues in further steps of the pipeline.
Is this a known issue? am I possibly doing something wrong? I tried searching the documentation but "INTERVAL" is not one of the expected varType options
Thank you in advance, Talya Dor (bioinformatician, Illumina)