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87 Open 98 Closed
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Issues list

filter_indels.pl vcf2 error
#294 opened Feb 7, 2025 by alkc
Fix the M955 special case
#287 opened Jan 21, 2025 by Jakob37
@alkc
ID-SNP calculations in ol' wgs
#285 opened Jan 10, 2025 by Jakob37
@Jakob37
Update Sentieon
#282 opened Jan 9, 2025 by Jakob37
@A97paupic
Update bcftools
#281 opened Jan 9, 2025 by Jakob37
1
@Jakob37
1
Update samtools
#280 opened Jan 9, 2025 by Jakob37
@A97paupic
Everything should be CRAM
#279 opened Jan 9, 2025 by Jakob37
@alkc
Deploy ol' wgs using Git
#271 opened Dec 13, 2024 by Jakob37
Update GATK
#270 opened Dec 12, 2024 by Jakob37
Peddy output into CDM
#266 opened Nov 26, 2024 by Jakob37
@alkc
Update AnnotSV and look over prescore_sv.pl
#265 opened Nov 22, 2024 by Jakob37
@ViktorHy
CLNSIG is not assigned to SVs
#264 opened Nov 22, 2024 by Jakob37
@ViktorHy
2
vcf-anno: Investigate poor matching of longer indels with clinvar VCF bug Something isn't working vep
#263 opened Nov 22, 2024 by alkc
2 tasks
Replace fastgnomad/annotate with vcf-anno
#262 opened Nov 22, 2024 by alkc
1
Version control and document annotate script
#261 opened Nov 22, 2024 by Jakob37
Make scout panel dump script deal with panels duplicated across institutes in scout
#259 opened Nov 20, 2024 by alkc
Missing overview plot in BAM output bug Something isn't working
#257 opened Nov 15, 2024 by Jakob37
Use "$id" for tagging processes where relevant rather than "$group"
#250 opened Nov 7, 2024 by Jakob37
Add pipeline git hash / version to sample versions.yml
#246 opened Oct 28, 2024 by alkc
Add loqusdb variant scoring for myeloid_const status: on hold
#242 opened Oct 23, 2024 by alkc
2 tasks
Convert SMN1 SMN2 variants to SV VCF call format
#241 opened Oct 17, 2024 by Jakob37
@alkc
-cohort30.vcf.gz file is actually .sam
#240 opened Oct 10, 2024 by Jakob37
Contamination for panels and wgs
#238 opened Oct 2, 2024 by ViktorHy
@A97paupic
1
Upload peddy parenthood results to CDM
#237 opened Oct 1, 2024 by alkc
4 tasks
@alkc
dry-run / annotation-only run of clinvar VCF crashes at peddy
#236 opened Oct 1, 2024 by alkc
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