Issues

• BLR appears to still be running despite generation of MultiQC report

  AfshinLab/BLR#93 · Filter by author ajdesalvio opened on Jul 25, 2025
  2

• crashes after "checkpoint extract_barcodes"

  AfshinLab/BLR#92 · Filter by author IlinaMargo opened on Apr 17, 2025
  12

• Load R before submitting SLURM batch job (and other necessary modules)

  AfshinLab/BLR#83 · Filter by author ajdesalvio opened on Sep 26, 2024
  1

• Improve documentation

  AfshinLab/BLR#81 · Filter by author pontushojer opened on Nov 3, 2023

• Detect sample sex from input

  AfshinLab/BLR#79 · Filter by author pontushojer opened on Oct 10, 2023

• Automatically filter out barcodes with too many molecules

  AfshinLab/BLR#78 · Filter by author pontushojer opened on Oct 2, 2023

• Add Haplotagging support

  AfshinLab/BLR#77 · Filter by author pontushojer opened on Oct 2, 2023

• Re-call SNVs after phasing

  AfshinLab/BLR#76 · Filter by author pontushojer opened on Oct 2, 2023

• Make use of molecule information in LinkFragments

  AfshinLab/BLR#75 · Filter by author pontushojer opened on Oct 2, 2023

• Test phasing with HapTree-X

  AfshinLab/BLR#74 · Filter by author pontushojer opened on Oct 2, 2023

• Rule map_sort sometimes fails for ema

  AfshinLab/BLR#73 · Filter by author pontushojer opened on Oct 2, 2023

• Remove tagbam for DBS and TELL-seq when mapping with EMA

  AfshinLab/BLR#72 · Filter by author pontushojer opened on Oct 2, 2023

• Test alternative phasing algorithm: SpecHap

  AfshinLab/BLR#71 · Filter by author pontushojer opened on Oct 2, 2023

• Update use of read groups

  AfshinLab/BLR#70 · Filter by author pontushojer opened on Oct 2, 2023

• Snakemake version >=6.5 does not schedule jobs optimally

  AfshinLab/BLR#69 · Filter by author pontushojer opened on Oct 2, 2023

• MultiQC 1.12 not compatible with BLR

  AfshinLab/BLR#68 · Filter by author pontushojer opened on Oct 2, 2023

• gatk HaplotypeCaller filters out QUAL < 30 by default

  AfshinLab/BLR#67 · Filter by author pontushojer opened on Oct 2, 2023