MethBat v0.11.0

Changes

• Modifies the segmentation algorithm to prevent large segments from spanning CpG data gaps. The new algorithm will automatically create segment break points between two consecutive CpGs that exceed a maximum gap threshold. This reduces segment size inflation around regions with low coverage and/or absent phasing information.
• Adds a CLI option --max-gap to control the maximum gap threshold, default: 1000 bp.

MethBat v0.10.1

Fixed

• Fixed a panic caused by low sample sizes in the compare command. These will now be flagged as InsufficientData.

MethBat v0.10.0

Changes

• Adds a CLI option --enable-haplotype-segmentation that will run segmentation on the individual haplotypes (H1 and H2) and save those segments in the output BED file. For example, an unmethylated region on haplotype 2 will have the label "H2_Unmethylated" (or "H2_U" if condensed).
• Adds a CLI option --enable-nodata-segments that will generate segments where haplotype data is missing. These will be flagged like "H1_NoData" (or "H1_ND" if condensed).

The following is an example of how these tracks might look in IGV:

MethBat v0.9.0

Changes

• Adds a new segmentation mode based on Circular Binary Segmentation. This mode generates a BED file of methylated, unmethylated, and ASM regions. The mode is executed with methbat segment ..., see README for more details.

Fixed

• Improved error handling for all CLI interfaces

Initial alpha release - MethBat v0.8.3

Changes

• Initial alpha release
• Includes initial version of HPRC background profiles