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Issues list

gatk HaplotypeCaller filters out QUAL < 30 by default
#248 by pontushojer was closed Oct 2, 2023
1
MultiQC 1.12 not compatible with BLR
#247 by pontushojer was closed Oct 2, 2023
1
Include software versions in report
#246 by pontushojer was closed Sep 2, 2022
Generate SV VCF as part of final output.
#245 by pontushojer was closed Dec 21, 2021
Snakemake version >=6.5 does not schedule jobs optimally
#244 by pontushojer was closed Oct 2, 2023
1
Rethink phaseblock length plot in report
#243 by pontushojer was closed Sep 30, 2021
3
starcode runs out of memory for large datasets
#242 by pontushojer was closed Sep 2, 2022
4
Make barcode merging configurable
#241 by pontushojer was closed Oct 2, 2023
3
Enable subsampling of input FASTQ
#240 by pontushojer was closed Oct 2, 2023
1
Update use of read groups
#239 by pontushojer was closed Oct 2, 2023
New phasing algorithm: SpecHap
#238 by pontushojer was closed Oct 2, 2023
How to use wfa2tenx or BLR_metagenomics?
#237 by YichaoOU was closed Mar 3, 2021
2
where is chr1mini.fasta?
#236 by YichaoOU was closed Feb 15, 2021
1
Rule map_sort sometimes fails for ema
#235 by pontushojer was closed Oct 2, 2023
Filter out barcodes not matching pattern.
#234 by pontushojer was closed Jan 21, 2021
1
Add phasing with HapTree-X
#232 by pontushojer was closed Oct 2, 2023
Add all parameters to configs?
#231 by pontushojer was closed Feb 9, 2021
1
Run for specific region only
#230 by pontushojer was closed Oct 2, 2023
Chunk specific runtime artefacts in clusterrmdup
#229 by pontushojer was closed Sep 30, 2020
1
3
Include workflow for how to merge and run processed BAMs
#228 by pontushojer was closed Sep 21, 2020
1
1
Filter for MAPQ
#227 by pontushojer was closed Sep 3, 2020
Limit phasing to only chr1-chr22 (+chrX if female)
#226 by pontushojer was closed Feb 18, 2021
1
blr plot command fails when posting job on uppmax
#225 by pontushojer was closed Aug 13, 2020
Speed up MultiQC
#224 by pontushojer was closed Nov 6, 2020
2
calculate_haplotype_statistics fails with HapCUT2 1.3.2
#223 by pontushojer was closed Aug 10, 2020
ProTip! Updated in the last three days: updated:>2025-03-07.