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Clinical-Genomics-Lund
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nextflow_wgs
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Rank model updates for VEP 111
#176
alkc
closed
5 months ago
0
Dealing with committed lab IDs in mody cf
#175
Jakob37
opened
5 months ago
0
GQC issue
#174
Jakob37
closed
5 months ago
1
Load MT frequencies into loqusdb
#173
Jakob37
closed
3 months ago
2
Reproducibility issue within same sample/group due to order of inputs to SVDB_merge
#172
alkc
opened
6 months ago
1
GATK GQC always cast to int to prevent genmod from ignoring it
#171
alkc
closed
6 months ago
3
`GQC` encoded as `float` disables `GATK` caller penalty
#170
alkc
closed
6 months ago
0
Starting from bam with modified group/sample ids fails at `build_mitochondrial_qc_json`
#169
alkc
opened
6 months ago
1
Add project pre-commit hooks
#168
alkc
opened
6 months ago
1
Add information on annotation dbs to GitHub documentation
#167
Jakob37
opened
6 months ago
0
Paths in scout yaml do not respect custom `--outdir`
#166
alkc
opened
6 months ago
0
Use tags for all processes
#165
Jakob37
opened
6 months ago
0
Update CADD indel to 1.7
#164
Jakob37
closed
6 months ago
1
Update CADD indel to v1.7
#163
Jakob37
opened
6 months ago
1
Complete the mody cf PR
#162
Jakob37
closed
3 months ago
0
Reproducible bwa K
#161
Jakob37
closed
4 weeks ago
3
Extract the SO/most_severe_consequence ranking from `modify_vcf_scout.pl` and keep in version control
#160
alkc
opened
6 months ago
0
Investigate if Phylops/phastcons can be retrieved from DBSNFP instead of external/custom VEP dbs.
#159
alkc
opened
7 months ago
0
Jw/clean up in versions
#158
Jakob37
closed
7 months ago
0
`[W::vcf_parse] Contig 'X' is not defined in the header. (Quick workaround: index the file with tabix.)` when loading wgs case into scout
#157
alkc
opened
7 months ago
0
Investigate Clinsig value missing internal representation warning when loading wgs case in scout
#156
alkc
opened
7 months ago
0
Investigate scout AF parsing error
#155
alkc
opened
7 months ago
4
Don't write /access/ symlink paths to case.yaml when running with `--dev`
#154
alkc
opened
7 months ago
1
Jw/update cadd
#153
Jakob37
closed
7 months ago
5
Update tiddit
#152
Jakob37
closed
2 months ago
1
Look over bwa-mem reproducibility issues
#151
Jakob37
closed
4 weeks ago
0
Update rank model and `modify_scout_vcf.pl` with new VEP 105 annotations
#150
alkc
closed
2 months ago
3
Change default handling of undefined annotations when selecting `most_severe_consequence` in `modify_scout_vcf.pl`
#149
alkc
opened
7 months ago
0
Update Gnomad
#148
Jakob37
closed
6 months ago
4
Run output diff script
#147
Jakob37
closed
6 months ago
0
Add version to genmod container name + move out of main.nf
#146
alkc
opened
7 months ago
1
Remove some old docs and rearrange repo to use new docs by default
#145
Jakob37
closed
7 months ago
0
Update fastp to 0.23.4
#144
alkc
closed
7 months ago
6
Update fastp version for speedup and reproducibility
#143
Jakob37
closed
4 months ago
2
Verification
#142
Jakob37
closed
5 months ago
2
Add software responsible to docs
#141
Jakob37
closed
7 months ago
0
Mito `GT` field mangled when breaking up multis
#140
alkc
opened
7 months ago
0
Set target scout institute in create_yaml through param
#139
alkc
opened
7 months ago
0
Can mutect2 be dropped in favor of sentieon only?
#138
alkc
closed
7 months ago
1
Bam entry point does not run DNAScope if ID != group
#137
Jakob37
closed
3 weeks ago
0
Add D4 coverage calculations
#136
Jakob37
closed
5 months ago
0
gzip the world (where applicable)
#135
alkc
opened
7 months ago
2
Document `split_normalize_mito` process
#134
alkc
opened
7 months ago
0
Add GQ field to mutect2 called VCF to facilitate loqusdb import
#133
ViktorHy
closed
3 months ago
0
Upgrade to VEP 111.0
#132
alkc
closed
5 months ago
16
Sentieon update
#131
Jakob37
closed
7 months ago
3
Update intersect file
#130
Jakob37
closed
7 months ago
4
Add changelog reminder github workflow
#129
alkc
closed
8 months ago
0
Update Sentieon to 2023 version (or check that the results are identical) - Latest February
#128
Jakob37
closed
5 months ago
0
Documentation into ReadTheDocs
#127
Jakob37
opened
8 months ago
0
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