The user manual section on splicing (from pg 63) provides an overview of this topic, as well as...
FAQs
How are splicing scores interpreted in AlamutTM Visual Plus?
AlamutTM Visual Plus includes a splicing module accessible from the variant panel that integrates...
Why are there differences between RefSeq and Ensembl transcripts and exons?
Ensembl and RefSeq transcripts differ in that Ensembl transcripts are mapped onto the reference...
Why are there differences in exon naming for some transcripts/genes?
Two different conventions are used for exon naming.Systematic Exon Numbering starts at 1 and...
Why are there differences in exon naming for some transcripts/genes?
Two different conventions are used for exon naming.Systematic Exon Numbering starts at 1 and...
Why are there sometimes mismatches between genes and transcripts (nucleotides highlighted in red on the transcript track)?
This is due to occasional genome/transcript sequence discrepancies, where the genome reference...
Why is the link to dbSNP on the GRCh37 build missing?
RefSeq displays GRCh38 as a default genome for all rsID links. On dbSNP variant pages, links for...
How can we have a negative genotype count with gnomAD?
We compute Genotype Count based on values from a gnomAD VCF. In some cases, we end up with...
Why do links to gnomAD not work with some variants?
gnomAD links are built based on the position, ref, and alt of the variant. In AlamutTM Visual...
Should I switch to the latest version of gnomAD?
The gnomAD v2 call-set contains fewer whole genomes than v3.1, but also contains a very large...
What version of gnomAD is used in AlamutTM Visual Plus?
gnomAD provides the following recommendation on which version to use: "gnomAD v2 is still our...
How are GnomAD filters used within AlamutTM Visual Plus?
By default, AlamutTM Visual Plus includes all available variants from GnomAD, irrespective of the...