v2.4.0

MutMap v2.4.0

What’s New

• Improved error handling with clearer messages for common failures.
• Added environment.yml for one-step environment setup.
• Improved plot export behavior to reduce clipped labels/text.

Quick Install

conda env create -f environment.yml
conda activate mutmap

v2.3.9

• Fixed an issue with BAM file input by incorporating samtools collate.

v2.3.8

What's new in this version:

• Colorblind-friendly plot colors: The default colors used in the generated plots have been updated to be more accessible for individuals with color vision deficiencies, ensuring better readability for everyone.

• Improved logging format: We have enhanced the log formatting during the execution of MutMap and MutPlot, providing clearer and more consistent output, making it easier to track the progress of the analysis.

• Automatic handling of large genome BAM indexing and VCF tabix errors: For large genomes like wheat, we’ve added automatic handling for errors during BAM indexing and VCF tabix creation. If samtools index fails, the script will automatically retry with samtools index -c. Similarly, if tabix fails, it will automatically retry with tabix -C.

• Extended BAM support: The script has been updated to ensure that when starting with BAM files, essential operations such as BAM filtering, fixmate, and markdup are performed automatically, ensuring consistency with workflows starting from FASTQ files.

• Updated environment variable settings: To prevent errors related to numpy imports and multithreading issues, we have adjusted the placement of environment variables like OMP_NUM_THREADS and USE_SIMPLE_THREADED_LEVEL3, providing a more stable runtime environment.

• New documentation files: We’ve added two new markdown files to the doc directory:

  • 01_MutMap_Commands_Breakdown.md: This file provides a detailed breakdown of the commands used in MutMap, helping users understand and utilize the tool more effectively.
  • 02_Guide_to_Build_SnpEff_DB.md: A guide to assist users in building a SnpEff database, offering step-by-step instructions for integrating SnpEff into their MutMap analysis.

v2.3.6

• Improve the README file and command options
• Added the options to change the colors in plots
• Fixed the bug in plotting function when the reference genome has more than 50 contigs.
  (Also, in the previous version, only the significant contigs were plotted, but the 50 longest contigs are plotted since this version)

v2.3.5

• Multiple testing correction has been deprecated.
• Added some modifications to avoid the potential errors in python multi-processing and java memory.

v2.3.4

• Fixed a multiprocessing error on Mac

v2.3.3

• Plot only significant contigs for contiguous reference genome (> 50 contigs) to avoid an error during plotting procedure.

v2.3.2

• Remove "-a" option during BCFtools concat. This update reduce the memory cost during the concatenation of VCFs.

v2.3.0

Update to v2.3.0

• To remove PCR duplicates, samtools fixmate & markdup commands included
• For faster read filtering, samtools view -f 2 -F 2048 used instead of the application of the flags 83,99,147,163
• New option "--format" included to change the figure format from "png"

v2.2.0

• Fixed the bug during plotting.