ddaneels

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ddaneels
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  • I have a question about the Funcotator tool. I saw in the resources that gnomAD is available. I was wondering if ESP6500 and 1000genomes are also included? Or does gnomAD also covers ESP6500 and 1000genomes? Because those two databases are listed a…
  • @davidben so you mean that I don't need to specify the parameter --af-of-alleles-not-in-resource 0.0000025 when I'm using --germline-resource af-only-gnomad.raw.sites.hg19.vcf.gz. In that way the default value of --af-of-alleles-not-in-resource is u…
  • Hi, I'm not sure that I understand the use of the --germline-resource and --af-of-alleles-not-in-resource parameters My input bam comes from a human tumor-only gene panel (20 genes). So I'm using the following parameters: --germline-resource af-o…
  • In your description you state: It's very important to use normals that are as technically similar as possible to the tumor ... Normals are typically derived from blood samples. We are dealing with tumor FFPE samples, would it then be best to create…
  • We seem to be getting somewhere. I was able to install version 3.6. Now I get the error MESSAGE: Key AC_Adj0_Filter found in VariantContext field FILTER at chr1:1375207 but this key isn't defined in the VCFHeader. We require all VCFs to have compl…
  • I tested it with with GATK3.4, that we had already installed. The error disappeared, but the program is not advancing. It's stuck at: ... INFO 16:52:13,526 GenomeAnalysisEngine - Strictness is SILENT INFO 16:52:16,120 GenomeAnalysisEngine - Downsamp…