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  • Hi Genevieve, We repeated the analysis with GATK 4.2.1 with --linked-de-bruijn-graph enabled and the variant now survives to the VCF! We are not sure yet if this is because the new version or becau...

  • Hi Genevieve, I ran this: gatk GenotypeGVCFs --output allsites.vcf --reference Homo_sapiens_assembly38.fasta --variant Sample_A.g.vcf.gz --include-non-variant-sites true --intervals chr20:4690000-4...

  • Hi Genevieve, I have attached a screenshot from IGV for the HaplotypeCaller bam, with the variant highlighted (from Sample A). How do you force the variant to be called by GenotypeGVCFs? Many thank...

  • Hi Genevieve, Thank you for your help! I have looked at the trouble shooting doc.  The expected variant was called at the site of interest in the GCVF (see above), but excluded from the VCF by Geno...