Version 1.2.0

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Important Note: This version is not backwards compatible with BISCUIT Version 0.3.16 and earlier.

Date Created:

• 30 January 2023

General changes:

• Copyright years updated.

Changes affecting specific subcommands/scripts:

• align:
  • MC (mate CIGAR) and MQ (mate quality) SAM auxiliary tags added to alignment output
• pileup:
  • Read 1 and Read 2 overlap is now determined by the MC tag. If MC tag is missing, read lengths are assumed to be the same.
• epiread:
  • Read 1 and Read 2 overlap is now determined by the MC tag. If MC tag is missing, read lengths are assumed to be the same.
  • Print statement for filtered epiBED lines (only F/x/P entries) is now behind the verbose (-v) flag.
  • epiBED and pileup output now match when using an unfiltered BISCUIT SNP BED as input (-B option) to biscuit epiread.
    • BISCUIT SNP BED file must be used in order to account for when methylation could be called in the case of an ambiguous C>T or G>A SNP. If not used, methylation levels might not match up between pileup and epiread.
    • Important note: The epiBED file required an overhaul to align the pileup and epiread output:
      • There are now always nine columns: 1) chromosome, 2) start, 3) end, 4) read name, 5) read number, 6) bisulfite strand, 7) CpG methylation RLE string, 8) GpC methylation RLE string ("." if BS-seq), and 9) short structural variants (SNPs/indels) RLE string.
      • SNPs/indels follow the same conventions as before in the variant RLE string. For the CpG and GpC RLE strings, "I" is used for insertions, "d" for deletions, and "x" for SNPs with no methylation status.
      • All methylation now occurs in the position it is found in the reference. Previously, methylation always was situated relative to the C position in the CG. Now, methylation will be noted at the C position for OT/CTOT (bisulfite strand +) and the G position for OB/CTOB (bisulfite strand -). This lines up with how methylation is accounted for in pileup.
    • Special thanks to the Brendel group at Indiana University for bringing up the difference between the epiBED results and pileup and providing additional testing.
  • Results for the old epiread format (-O) and the pairwise format (-P) remain the same as before. Therefore, results matching pileup are not guaranteed. These formats remain for legacy analyses and it is suggested that analyses move to the epiBED format.

Bug Fixes:

• Issue #26 fixed (incorrect number of degrees of freedom in biscuit asm). Reported by Volker Brendel.
• Issue #28 (segfault when G in a CG is first base of a OB/CTOB read pair). Reported by Volker Brendel.
• Issue #32 (incorrect number of threads requested for GNU parallel). Reported by Nick Semenkovich. Fixed by Nick Semenkovich.