MethBat v0.13.3

Changes

• Added support for parsing pb-CpG-tools files that have been compressed (i.e., {prefix}.combined.bed.gz) to save storage

MethBat v0.13.2

Fixed

• Modified the checker for profile and segment modes to allow for missing hap1 and hap2 BED files. This is most common when pb-CpG-tools is run on unphased datasets. A warning will be produced in the log if these files are missing, and haplotype-specific data will not be generated.

MethBat v0.13.1

Changes

• Adds two haplotype-specific tracks for methbat segment:
  • {OUT_PREFIX}.hap1.bedgraph - Contains the underlying methylation values for haplotype 1 for each segmented region
  • {OUT_PREFIX}.hap2.bedgraph - Same as above, but for haplotype 2

Fixed

• Fixed an issue where the BEDGRAPH outputs from methbat segment were reporting median values instead of the indicated mean values. This change did not alter the segmentation itself. However, since the value associated with each segment changed, the reported regions in {OUT_PREFIX}.meth_regions.bed may be altered to reflect the correct, mean values.

MethBat v0.13.0

Changes

• Beta release of a new signature mode, methbat signature, that will identify regions with different combined methylation in a case-control population. Greater details on usage can be found in the documentation for signature mode.
• User guide documentation has been re-organized into sections based on functionality for easier use

Fixed

• Fixed an issue where the mean methylation metrics for methbat profile were aggregated with unequal weights
• Updated the provided meth_profile_model.tsv background file to use the correct equal weights. The changes across most loci are relatively small, with the average delta of ~1% for avg_abs_meth_deltas and ~2% for avg_combined_methyls.

MethBat v0.12.0

Changes

• Breaking change: The methbat segment output --output-segments has been changed to --output-prefix. It will now generate the following output files with extensions of the given prefix:
  • {OUT_PREFIX}.meth_regions.bed - The BED file with merged regions, same output as the previous --output-segments option
  • {OUT_PREFIX}.combined_methyl.bedgraph - New output that contains the underlying combined methylation values for each segmented region
  • {OUT_PREFIX}.asm.bedgraph - New output that contains the underlying ASM values for each segmented region

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