Manuel Holtgrewe comments

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                                            Manuel Holtgrewe

Allow for manually correcting HGVS Notation/Call for an annotated variant

Also requires updates to baserow ETL scripts, thus would not be as helpful as needed right now. Postponing.

Variant DEL-grch37-5-150175225-150181898 exonic, but overlaps 3'utr only

Seqvars mehari has separation of UTR exonic/intronic, needs to be ported to SVs.

Implement multiallelic variants/variant normalization

VEP can handle it so should we...

Improved types for Vue Tanstack Query

Actually, `MaybeRefOrGetter` should be used and `toValue(value)` can be used to resolve this.

Improved types for Vue Tanstack Query

@mrlubos As always, I'm grateful for the work you put into this wonderful library. Is there any timeline regarding a fix to this?

java.lang.IllegalStateException in JointGermlineCNVSegmentation

As a follow-up, I now get incorrect ploidy calls and subsequent ploidy in the CNV call files for ~10 out of ~300 exome data sets enriched with Agilent V8 chemistry....

Mehari needs better handling of transcripts without stop codon in CDS, e.g., NM_001291324

Curious, all transcripts of `HGNC:29279` are affected by this but UCSC shows RefSeq transcript alignments.

Mehari needs better handling of transcripts without stop codon in CDS, e.g., NM_001291324

OK, this appears to be legit by the data ... ``` # grep 'NM_001377448|NM_001291324' ~/mehari-data-tx/pass-1/txs.bin.zst.report Skipping transcript NM_001291324.3 because of missing stop codon in translated CDS Skipping transcript NM_001377448.1 because...

Mehari needs better handling of transcripts without stop codon in CDS, e.g., NM_001291324

There are 139 such transcripts, see below. Most probably, we cannot easily resolve this for GRCh37. ``` # grep 'because of missing stop codon' ~/mehari-data-tx/pass-1/txs.bin.zst.report | wc -l 139 #...

exon coverage

I agree, we need to find a solution with either pre-compute for all exon or retrieve online from BAM.