Which reference genome is being used to align the reads?

Reference genome

Reference genomes hg19 and hg38 are used for standard chromosomes. The preferred reference genome can always be selected when launching a new analysis.

The following alternate loci were removed from hg19 :

  • chr4_ctg9_hap1
  • chr6_apd_hap1
  • chr6_cox_hap2
  • chr6_dbb_hap3
  • chr6_mann_hap4
  • chr6_mcf_hap5
  • chr6_qbl_hap6
  • chr6_ssto_hap7
  • chr17_ctg5_hap1

Please, note that we do not handle ALT contigs of the hg38 reference genome version at the moment.

Mitochondrial genome

With regard to the mitochondrial genome, in VarSome Clinical when the analysis is launched from fastq sample(s), using either hg19 or hg38, any mitochondrial sequences will be aligned to the standard mitochondrial genome (GenBank number: NC_120920.1), which is included in the hg38 human genome. For more details please see the Mitochondrial genome versions

Pseudoautosomal regions

The pseudoautosomal regions of chromosome Y have been masked in hg19. For hg38 this has not been applied yet.

Should I use hg19 or hg38?

  • When starting your analysis from VCF: the reference genome must be the same as the one it was used in the mapping and variant calling pipeline that generated the VCF files.
  • If you are using a specific assay, please make sure the assay version is available for the reference genome you want to select. Please, contact support if you are not sure about this.
  • If you don't know which genome should you select, the recommended option is hg38. This is a corrected and improved version of hg19. You should use the newer and better assembly.