MIP

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Variant not called in MIP-analysis

3

Issue: Case F0059468 (cust002) have a pathogenic variant in KRT6B that was not called in the WGS analysis. We found out that our patient's sister with the same disease was...

AnnHam

SV annotation - merge order looses some translocation annotation

4

VEP annotation should precede merger of SV files. Caller VCFs (manta, TIDDIT) have separate (linked) entries for both ends of a translocation. While this may be redundant, VEP is not...

dnil

PEX6 managed 3'-variant not shown

15

Hi! I noticed that in our case 23289, the 3'UTR polymorphism c.*442_445delTAAA is visible in Scout, but not shown on the front page, although we have the variant saved as...

MUebe

Show local variant archive date also on SV pages

5

The little hover over local observations archive only shows the date on SNV pages. 😅

dnil

**Is your feature request related to a problem? Please describe.** MEIs appear unsorted in scout. Even a simple scoring would help organise triage. **Describe the solution you'd like** Score variants...

dnil

Not called deletion in mtDNA

5

There is a mtDNA deletion in case 23103, which is not called in Scout. We have confirmed it with MLPA and also sequenced the breakpoints by sanger sequencing. I recently...

1ctw

**Describe the bug** Currently the most severe consequence selection for MEI is a bit off. It can select non coding transcript consequences over coding sequence ones with the same effect,...

dnil

most severe consequence polypyrimidine stretch

8

**Describe the bug** We are seeing more issues with the most severe consequence. We recently fixed the clinical filter in scout (https://github.com/Clinical-Genomics/scout/issues/3858) to allow showing these nice little fellows, but...

dnil

Support for hg38 from fastq to ranked variants

6

**Recipes** - [x] fastqc - [x] bwa_mem - [x] picardtools_mergesamfiles - [x] markduplicates - [x] gatk_baserecalibration - [x] chanjo_sexcheck - [x] samtools_subsample_mt - [x] tiddit_coverage - [x] sambamba_depth (test new...

henrikstranneheim