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77 Open 78 Closed
77 Open 78 Closed
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Issues list

Add pipeline git hash / version to sample versions.yml
#246 opened Oct 28, 2024 by alkc
Missing svdb_origin SV vcf tag leads to bad caller info for merged variants in scout
#244 opened Oct 28, 2024 by alkc
1
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
Upload peddy parenthood results to CDM
#237 opened Oct 1, 2024 by alkc
4 tasks
dry-run / annotation-only run of clinvar VCF crashes at peddy
#236 opened Oct 1, 2024 by alkc
modify_vcf_scout.pl bugs out when processing VCF without fields after INFO field bug Something isn't working
#234 opened Sep 27, 2024 by alkc
bam-only starts with updated sample ids crash due to sample id mismatch between ped and vcf in inher_models + other mismatches bug Something isn't working
#233 opened Sep 26, 2024 by alkc
vep_sv crashes pipeline if there are no records in output from SVDB merge process
#230 opened Sep 20, 2024 by alkc
@alkc @A97paupic
Crash early if sample ID mismatches with ID in VCF header quality of life
#229 opened Sep 18, 2024 by Jakob37
Annotation only workflow crashes due to missing Pathogenicity INFO field (MT specific) bug Something isn't working
#227 opened Sep 13, 2024 by Jakob37
Include compound scores also for singles bug Something isn't working
#226 opened Sep 9, 2024 by Jakob37
@Jakob37
d4_file not added to yaml in bam-only starts
#223 opened Aug 29, 2024 by alkc
Group id, group, type and sex into a meta object
#222 opened Aug 22, 2024 by Jakob37
Test mimisbrunnr as a extra layer of clinical significance for CNVs
#217 opened Aug 15, 2024 by ViktorHy
2
Order of VCFs to SVDB merge not consistent between subsequent reruns of same sample bug Something isn't working
#216 opened Aug 14, 2024 by alkc
1
Downsample mito bams to prevent eklipse crashes enhancement New feature or request
#215 opened Aug 12, 2024 by alkc
Add restart rules to processes enhancement New feature or request
#214 opened Aug 12, 2024 by alkc
Add flag to stop pipeline when bam + qc has been generated enhancement New feature or request
#212 opened Jul 26, 2024 by alkc
2 of 7 tasks
1
@alkc
GERP annotations missing bug Something isn't working
#205 opened Jun 27, 2024 by alkc
1
Profile for solid tumors
#203 opened Jun 11, 2024 by Jakob37
Memory usage markdup and dnascope
#200 opened May 30, 2024 by ViktorHy
Control CPU / memory allocations from config
#197 opened May 22, 2024 by Jakob37
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