Hello GATK team,
I have called variants with Mutect2 and filtered with FilterMutectCalls, generating a final vcf.gz file. When I upload this file in IGV I get this error:
I have tried to view it with bcftools and everything seems fine to me.
If I decompress with:
bcftools view filename.var.gz > filename.vcf
It uploads and opens without any issue.
I was wondering if you have an idea of what is happening here.
GATK version used: 126.96.36.199
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