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FrickTobias
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BLR
MIT License
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gatk HaplotypeCaller filters out QUAL < 30 by default
#248
pontushojer
closed
1 year ago
1
MultiQC 1.12 not compatible with BLR
#247
pontushojer
closed
1 year ago
1
Include software versions in report
#246
pontushojer
closed
2 years ago
0
Generate SV VCF as part of final output.
#245
pontushojer
closed
2 years ago
0
Snakemake version >=6.5 does not schedule jobs optimally
#244
pontushojer
closed
1 year ago
1
Rethink phaseblock length plot in report
#243
pontushojer
closed
3 years ago
3
starcode runs out of memory for large datasets
#242
pontushojer
closed
2 years ago
4
Make barcode merging configurable
#241
pontushojer
closed
1 year ago
3
Enable subsampling of input FASTQ
#240
pontushojer
closed
1 year ago
1
Update use of read groups
#239
pontushojer
closed
1 year ago
0
New phasing algorithm: SpecHap
#238
pontushojer
closed
1 year ago
0
How to use wfa2tenx or BLR_metagenomics?
#237
YichaoOU
closed
3 years ago
2
where is chr1mini.fasta?
#236
YichaoOU
closed
3 years ago
1
Rule map_sort sometimes fails for ema
#235
pontushojer
closed
1 year ago
0
Filter out barcodes not matching pattern.
#234
pontushojer
closed
3 years ago
1
Enble lariat as mapper for 10x and stLFR reads.
#233
pontushojer
opened
4 years ago
0
Add phasing with HapTree-X
#232
pontushojer
closed
1 year ago
0
Add all parameters to configs?
#231
pontushojer
closed
3 years ago
1
Run for specific region only
#230
pontushojer
closed
1 year ago
0
Chunk specific runtime artefacts in clusterrmdup
#229
pontushojer
closed
4 years ago
3
Include workflow for how to merge and run processed BAMs
#228
pontushojer
closed
4 years ago
1
Filter for MAPQ
#227
pontushojer
closed
4 years ago
0
Limit phasing to only chr1-chr22 (+chrX if female)
#226
pontushojer
closed
3 years ago
0
blr plot command fails when posting job on uppmax
#225
pontushojer
closed
4 years ago
0
Speed up MultiQC
#224
pontushojer
closed
3 years ago
2
calculate_haplotype_statistics fails with HapCUT2 1.3.2
#223
pontushojer
closed
4 years ago
0
Update hapcut2 to version 1.3.2
#222
pontushojer
closed
4 years ago
0
rule concat_molecule_stats fails if one or more TSVs are empty
#221
pontushojer
closed
4 years ago
1
Update docs for MI tag - no longer unique
#220
pontushojer
closed
4 years ago
0
EMA trims barcodes to 16 bp
#219
pontushojer
closed
4 years ago
1
Overclustering in clusterrmdup
#218
pontushojer
closed
4 years ago
6
Stats to include in final report
#217
pontushojer
closed
3 years ago
1
10x integration only for EMA at the moment
#216
pontushojer
closed
4 years ago
0
Rewrite `buildmolecules` and `filterclusters` to synchronise information over chunks.
#215
pontushojer
closed
4 years ago
0
Rewrite `clusterrmdup` to synchronise information over chunks.
#214
pontushojer
closed
4 years ago
0
Investigate steps to skip in post-mapping processing for non-BLR technologies
#213
pontushojer
closed
3 years ago
1
Make use of molecule information in LinkFragments
#212
pontushojer
closed
1 year ago
1
Call SNVs after phasing
#211
pontushojer
closed
1 year ago
0
Versioning
#210
pontushojer
closed
4 years ago
1
Log files should not contain progress bars
#209
marcelm
closed
4 years ago
0
samtools sort should write its temporary files to /tmp
#208
marcelm
closed
4 years ago
0
Make test data creation reproducible
#207
marcelm
closed
3 years ago
1
The tests are too slow
#206
marcelm
closed
4 years ago
1
Parallelize by chromosome
#205
marcelm
closed
4 years ago
1
Add platform support
#204
pontushojer
closed
1 year ago
4
EMA adds separate RG
#203
pontushojer
closed
4 years ago
1
Minimap2 fails due to zero length reads
#202
pontushojer
closed
4 years ago
0
Handle Tn5-overlaps in buildmolecules.
#201
pontushojer
closed
4 years ago
1
Add pytest for blr trim and demultiplex.
#200
pontushojer
closed
4 years ago
2
Plot figures for summary report
#199
pontushojer
closed
4 years ago
0
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