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22 Open 34 Closed
22 Open 34 Closed
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Issues list

Enable BAM and VCF files as input for GenErode enhancement New feature or request
#76 opened Apr 8, 2024 by verku
@verku
Check that last line of GERP and VCF file is processed by gerp_derived_alleles.py bug Something isn't working next version Include this issue into the next pipeline version
#75 opened Mar 12, 2024 by verku
@verku
Add note to documentation about MapDamage2 rescale creating biases
#74 opened Feb 20, 2024 by verku
@verku
Fix minimum overlap for read merging in fastP bug Something isn't working next version Include this issue into the next pipeline version
#73 opened Jan 29, 2024 by verku
@verku
Update Snakemake to v8 next version Include this issue into the next pipeline version
#72 opened Jan 29, 2024 by verku
@verku
Double check if sorting of BAM and VCF files is strictly necessary enhancement New feature or request
#71 opened Jan 29, 2024 by verku
@verku
ANGSD error estimation enhancement New feature or request next version Include this issue into the next pipeline version
#70 opened Jan 23, 2024 by verku
Check how slurm profile handles group jobs bug Something isn't working next version Include this issue into the next pipeline version
#69 opened Jan 17, 2024 by verku
@verku
filter_mpile.py does not keep first and last nucleotide in a read bug Something isn't working next version Include this issue into the next pipeline version
#68 opened Jan 15, 2024 by verku
@verku
Update gerp_derived_alleles.py to work with phased genotypes enhancement New feature or request next version Include this issue into the next pipeline version
#67 opened Jan 15, 2024 by verku
@verku
Mapping of historical samples: make bwa aln parameter -n available in config file enhancement New feature or request next version Include this issue into the next pipeline version
#65 opened Dec 18, 2023 by verku
@verku
Add optional (?) second deduplication step between final merging and indel realignment for historical samples next version Include this issue into the next pipeline version
#64 opened Dec 12, 2023 by verku
@verku
Add GenErode to Workflowhub
#60 opened Oct 10, 2023 by verku
@verku
Filtering for biallelic sites does not remove sites with fixed derived variants enhancement New feature or request
#55 opened Sep 29, 2023 by verku
@verku
Problems running pipeline in Uppmax using the rhinos test dataset and slurm profile
#50 opened Jul 17, 2023 by apfuentes
2
rule multiqc_historical_raw: Stuck on 'Searching' bug Something isn't working
#49 opened May 12, 2023 by johannanvs
13
Add slurm profile to repository that works with Snakemake version in the conda environment enhancement New feature or request
#43 opened Mar 1, 2023 by verku
@verku
fastp can get memory issues enhancement New feature or request
#29 opened Sep 20, 2022 by verku
@verku
Rewrite memory allocation for java-based tools (e.g. qualimap) enhancement New feature or request
#26 opened Sep 1, 2022 by verku
@verku
Implement shadow rules for some rules (e.g. repeatmodeler) enhancement New feature or request
#3 opened Mar 1, 2022 by verku
@verku
2
Add some basic statistics on GERP scores to pipeline report for threshold decisions enhancement New feature or request
#2 opened Mar 1, 2022 by verku
@verku
Make threshold for Froh calculations adjustable in configuration enhancement New feature or request
#1 opened Mar 1, 2022 by verku
@verku
ProTip! no:milestone will show everything without a milestone.