1bd2b1f3f86df6284bc45e1075fe011d215d1d78 abenetpa Thu May 21 09:19:55 2020 -0700 correct typos as in refs #25424 diff --git src/hg/makeDb/trackDb/human/dbVarConflict.html src/hg/makeDb/trackDb/human/dbVarConflict.html index 917063d..11e5a5c 100644 --- src/hg/makeDb/trackDb/human/dbVarConflict.html +++ src/hg/makeDb/trackDb/human/dbVarConflict.html @@ -1,66 +1,66 @@

Description

The track NCBI dbVar Curated Common SVs: Conflicts with Pathogenic highlights loci where common copy number variants from nstd186 (NCBI Curated Common Structural Variants) overlap with structural Variants with clinical assertions, submitted to ClinVar by external labs (Clinical Structural Variants - nstd102).

Overlap in the track refers to reciprocal overlap between variants in the common (NCBI Curated Common Structural Variants) versus clinical (ClinVar Long Variants) tracks. Reciprocal overlap values can be anywhere from 10% to 100%.

For more information on the number of variant calls and latest statistics for nstd186 see Summary of nstd186 (NCBI Curated Common Structural Variants).

Display Conventions and Configuration

Items in all subtracks follow the same conventions: items are shaded according to variant type. Red for copy number loss or deletion, blue for copy number gain or duplication and violet for copy number variation. Mouseover on items indicates Allele Frequencies (AF).

All tracks can be filtered according to the variant lenth and type of variant. The variant overlap filter defines four bins within that range from which the user can choose.

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Data Acces

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Data Access

The raw data can be explored interactively with the Table Browser, or the Data Integrator. For automated analysis, the data may be queried from our REST API.

The data can also be found directly from the dbVar nstd186 data access. For questions about dbVar track data, please contact dbvar@ncbi.nlm.nih.gov.

Credits

Thanks to the dbVAR team at NCBI, especially Timothy Hefferon for technical coordination and consultation, -and to Christopher Lee, Anna Benet-Pages, and Maximilian Haeussler of the Genome Browser team for -engineering the track display. +and to Christopher Lee, Anna Benet-Pages, and Maximilian Haeussler of the Genome +Browser team for engineering the track display.

References

Lappalainen I, Lopez J, Skipper L, Hefferon T, Spalding JD, Garner J, Chen C, Maguire M, Corbett M, Zhou G et al. DbVar and DGVa: public archives for genomic structural variation. Nucleic Acids Res. 2013 Jan;41(Database issue):D936-41. PMID: 23193291; PMC: PMC3531204