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Clinical-Genomics / scout

VCF visualization interface
https://clinical-genomics.github.io/scout
BSD 3-Clause "New" or "Revised" License
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Callers not showing again on somatic SVs? #3620

Closed dnil closed 2 years ago

dnil commented 2 years ago

Report from @khurrammaqbool; seems callers have gone missing again on the variant page. We've seen this on the RD side, but are tracking a current MIP issue for that as well so...

dnil commented 2 years ago

BALSAMIC is using a set tag from SVDB. Example from bosssponge:


1       3536163 DEL00000001     G       <DEL>   1200    PASS    PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.9.1;END=3536196;PE=0;MAPQ=0;CT=3to5;CIPOS=-3,3;CIEND=-3,3;SRMAPQ=60;INSLEN=0;HOMLEN=3;SR=20;SRQ=1;CONSENSUS=CACGTGTCGAGAGAGGGGCCTGGTGGGAAGAGATTGCATCATGGGGGCAGATTTCTCCCTTGCTGTTCTCGTGATAGTCAGTTCTCAGGAGATCTGATGGTTTAAATGTGTGGCTTCCCCTTCATCTTCCGCCATGACTGTAAGTTTCCTGAGGCCTCCCCAGCCGGGTGTAATGGTGA;CE=1.97071;set=dellysv;dellysv_CHROM=DEL00000001|1;dellysv_POS=DEL00000001|3536163;dellysv_QUAL=DEL00000001|1200;dellysv_FILTERS=DEL00000001|PASS;dellysv_SAMPLES=DEL00000001|TUMOR|GT:0/1|GL:-365.97:0:-19.2806|GQ:10000|FT:PASS|RCL:2449|RC:892|RCR:1298|RDCN:0|DR:0|DV:0|RR:16|RV:112;dellysv_INFO=DEL00000001|PRECISE|SVTYPE:DEL|SVMETHOD:EMBL.DELLYv0.9.1|END:3536196|PE:0|MAPQ:0|CT:3to5|CIPOS:-3:3|CIEND:-3:3|SRMAPQ:60|INSLEN:0|HOMLEN:3|SR:20|SRQ:1|CONSENSUS:CACGTGTCGAGAGAGGGGCCTGGTGGGAAGAGATTGCATCATGGGGGCAGATTTCTCCCTTGCTGTTCTCGTGATAGTCAGTTCTCAGGAGATCTGATGGTTTAAATGTGTGGCTTCCCCTTCATCTTCCGCCATGACTGTAAGTTTCCTGAGGCCTCCCCAGCCGGGTGTAATGGTGA|CE:1.97071;svdb_origin=dellysv;CSQ=deletion|downstream_gene_variant|MODIFIER|RP11-46F15.2|ENSG00000238260|Transcript|ENST00000435049|antisense|||||||||||3558|-1||deletion|Clone_based_vega_gene||YES||||||||||||Ensembl||||||||||||||||||||||||||||||||||||||||,deletion|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000249933|||||||||||||||deletion|||||||||||||||||||||||||||||||||||||||||||||||||||||||      GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-365.97,0,-19.2806:10000:PASS:2449:892:1298:0:0:0:16:112```
dnil commented 2 years ago

Ok, my current hypothesis is its general, but fortunately not since too long:

https://github.com/Clinical-Genomics/scout/pull/3508

The add_callers() is nice refactor and all, but it is never called.

dnil commented 2 years ago

I'll make a PR.. Intuition says if this is actually called, things should go back to normal. But it seems likely all variants loaded after that was released. It is changelogged as appearing in 4.57.4 but seems the merge was later. I would bet it went live with 4.58 - correct? That would be 30 Aug.

https://github.com/Clinical-Genomics/scout/blob/d10900416e3417c818818b4aad9b56373ec558b1/scout/build/variant/variant.py#L282

northwestwitch commented 2 years ago

I think you are correct, merging dates is after the release of 4.57.4

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