VarSome Clinical version 8 released

Posted by Tomas Kucera on Nov 11, 2019 4:36:00 PM

VarSome Clinical Version 8

We are proud to present the latest version of VarSome Clinical with the following new features and improvements.

Introduction to VarSome Clinical

Updates & Improvements

  • Third-party software versions:
    • BCFtools 1.9
    • Bedtools 2.29.0
    • Delly 0.8.1
    • ExomeDepth 1.1.2
    • Fastqc 0.11.5
    • Picard Tools 2.20.6
    • Samtools 1.9
    • Sentieon Genomics suite 201808.08
    • VCFtools 0.1.15
  • We have modified our version of hg19 to map reads to the revised Cambridge Reference Sequence (rCRS, NC_012920, [1]) for mitochondrial variants. This is the standard human mtDNA sequence [2] used in the field and is already included as the mitochondrial genome in hg38. Analysis from user-provided VCF files containing the original hg19 version will also be annotated.
  • We significantly enhanced the VarSome Clinical API endpoints and documentation.
  • ACMG Classification. Improvements for clinical users who have gene-specific overrides, such as preferred transcript.
  • Recently updated databases: ClinVar, AACT, GHR, PanelApp, GWAS catalog, CGD and more. gnomAD v3.0 for hg38 to follow soon.
  • For hg19, we now map mitochondrial variants and transcripts both to chrM (the mitochondrial chromosome in the default hg19) and MT (the rCRS mentioned above). Please read here for more information. We are working on providing support for MitoMap soon.

In conclusion

As ever, we hope that you find VarSome useful, and we are continually striving to improve the platform. Do please contact us if you notice any issues or have suggestions on how to improve the platform.

References

[1] https://www.ncbi.nlm.nih.gov/nuccore/251831106

[2] https://www.mitomap.org/foswiki/bin/view/MITOMAP/MitoSeqs

Learn about VarSome Clinical

Topics: Platform Updates

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