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Add basic statistics for the filtered table in echo command.
This could include for example:
- [ ] number of variants
- [ ] number of samples
- [ ] number of genes
- [ ] het / hom counts
- [ ] t…
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Hello,
The genomic positions of variants are not identical between the *.vcf output and the standard *.aldy output. The positions in the VCF file are correct, but the output in the *aldy file is alw…
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We needed to remove an institute, and found no Scout command-line way to do it. This led to some issues where we at first didn't manage to properly remove all the references from the mongo db.
It w…
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Hi guys,
A number of additional scripts are provided (in the scripts and tools directories) for converting or analysing the PIRATE outputs.
I am using the ones to convert and run treeWas (pangenom…
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Hi,
I tried to retrieve additional information from gene_summary but some information of genes appear missing.
Working example:
`gemini query -q "select synonym from gene_summary where gene='ARTEM…
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`chr19 39706584 Minda_67 N . PASS SVLEN=10847666;SVTYPE=DEL;SUPP_VEC=PB_severus_DEL3306,PB_r_198,ONT_severus_DEL3735,ONT_ID_51104_2,ONT_r_120,ILL_MantaDEL:247507:0:1:0:0:0,PB_ID_62347_2,ILL_160549738…
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`chr15 98348348 Minda_47 N . PASS SVLEN=460879;SVTYPE=DUP;SUPP_VEC=ILL_MantaDUP:TANDEM:223247:0:1:0:0:0,ILL_gridss240bf_60h,ONT_severus_DUP2603,PB_ID_20435_2,PB_r_130,ONT_ID_72365_2,ONT_r_96,PB_Sniff…
jzook updated
2 weeks ago
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Entrez sometimes moves genes to a different/new entrez ID: E.g. SMIM44 (entrez ID 122152363) has been replaced with entrez ID 122405565. We currently have both in the database but they should probably…
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We moved to rankscore, but raw scores are used in ACMGv4 in PP3_supporting
Check out if any others are used
We should also run eg REVEL as a tool instead of dbNSFP
If not on the short variants then…