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Published 20 hours ago • verified publisher icon Illumina

FILTER 'HighDepth' is not defined in the header

Open ChristopheLegendre opened this issue 5 years ago • 1 comments

Hi Strelka2 Team,

I am using the release strelka-2.9.10

After running strelka in a somatic way for whole genome, we tried to annotate the strelka's vcf with snpEff; That tool (snpEff) showed us that one of the FILTER value is not defined in the header [W::vcf_parse] FILTER 'HighDepth' is not defined in the header

Questions

  • Could you add the description of HighDepth in the strelka2's vcf header?
  • What read depth value does trigger the HighDepth filter to be added to the FILTER column?

ChristopheLegendre avatar Jun 05 '19 21:06 ChristopheLegendre

This is strange. When the EVS is enabled (default), the HighDepth filter won't be applied and there will be no description in the header. If the EVS is disabled (--disableEVS), a description "Locus depth is greater than 3x the mean chromosome depth in the normal sample" will be added to the header.

Can you send me the Strelka commands and the VCF?

sangtaekim avatar Jun 07 '19 21:06 sangtaekim