Added
- Class I HLA variants and frequencies mapped with hla-mapper.
- Mobile insertion elements (MEIs) and frequencies detected with MELT.
Added
- Pop-up box of flags updated with WGS cohort thresholds leading to variant flags.
- Added Depth of Coverage graphs.
Added
- Variants from whole-genome sequencing dataset of 1,171 individuals from SABE cohorts in hg38 reference.
- Dropdown next to search engine to select between SABE-1171-WGS (hg38) OR SABE-609-WES (hg19) upon searching.
- External link in each variant to NCBI Reference SNP (rs) Report website.
- Home and About pages updates.
Added
- Exonic/Splicing and GATK filter boxes.
- Autocomplete of the gene name from 3rd letter onwards.
- Variant counter per queried result, prior to checking filter boxes.
Changes
- Layout of the page 'Search'.
- Gene search returns the range of genomic positions where the gene is nested, therefore occasionally retrieving variants annotated as
being from overlapping genes; Check Annovar's rules for annotation hierarchy regarding predicted consequence.
- Column header emphasizing that predicted consequences are annotated in genomic left aligned orientation.
Added
- 'Reference: hg19' label over search box.
- Option to export current table to excel or csv.
Changes
- The reported number of high confidence variants in the 'About' page (GATK PASS flags and excluding CEGH-USP FDP/FAB flags).