1. 09 Mar, 2021 1 commit
  2. 02 Mar, 2021 1 commit
  3. 07 Jan, 2021 1 commit
  4. 07 Aug, 2020 1 commit
    • van den Berg's avatar
      Add an option to restrict BaseRecalibration · 095305f0
      van den Berg authored
      The base recalibration step of the pipeline can take up to 7 hours for
      WGS samples, which is a significant part of the total run time.
      
      The developers of GATK state that BQSR requires at least 100M bases per
      read group: "We usually expect to see more than 100M bases per read
      group; as a rule of thumb, larger numbers will work better."
      
      A human WGS sample with an average read depth of 43x has almost 1300
      times that amount of bases. The analysis of these samples would be sped
      up greatly by restricting BQSR to a single chromosome.
      095305f0
  5. 24 Jun, 2020 1 commit
  6. 23 Jun, 2020 1 commit
    • van den Berg's avatar
      Add picard DuplicationMetrics to stats.json · 50e50edd
      van den Berg authored
      Unfortunately, this adds a limitation on the sample names that can be
      used with Hutspot, since the naming of the samples in the multiQC parsed
      output of picard MarkDuplicates is partly ambiguous.
      
      This limitation has been added to the readme, and a check has been added
      to the pipeline snakefile to throw an error when overlapping sample
      names are detected.
      50e50edd
  7. 03 Jun, 2020 2 commits
    • van den Berg's avatar
      Fix table formatting in Readme · 2f6685fc
      van den Berg authored
      2f6685fc
    • van den Berg's avatar
      Rename bedfile to targetsfile · d82c4932
      van den Berg authored
      Hutspot now supports two bed files to calculate coverage. One is the
      `targetsfile`, which was called `bedfile` before, and holds the targets
      of the capture kit. The other one is `baitsfile`, which holds the bait
      locations of the capture kit.
      
      It is possible to specify only the `targetsfile`, but if you specify the
      `baitsfile`, the `targetsfile` must be specified as well, since both are
      required by picard HsMetrics.
      
      Also added a test for invalid configuration files, and shortened the
      jsonschema validation error to only show the human readable message.
      d82c4932
  8. 30 Apr, 2020 1 commit
  9. 29 Apr, 2020 1 commit
  10. 16 Apr, 2020 2 commits
  11. 06 Apr, 2020 1 commit
  12. 13 Jan, 2020 1 commit
  13. 29 Aug, 2019 2 commits
  14. 28 Aug, 2019 1 commit
  15. 21 Jun, 2019 1 commit
  16. 31 May, 2019 1 commit
  17. 29 May, 2019 1 commit
  18. 28 May, 2019 2 commits
  19. 22 May, 2019 1 commit
  20. 30 Apr, 2019 1 commit
  21. 28 Mar, 2019 1 commit
  22. 21 Mar, 2019 2 commits
  23. 12 Mar, 2019 2 commits
  24. 26 Feb, 2018 1 commit
  25. 19 Jan, 2018 1 commit
  26. 30 Nov, 2017 5 commits
  27. 29 Nov, 2017 4 commits