v2.0.0

[release v2.0.0] - 2023-12-05

What's new

• Enable raw fastq data filtering by using SOAPnuke.
• Enable to create pipeline for WES or other kinds of capture sequencing data.
• Add Sentieon mudules. Enable to create WGS/capseq analysis pipeline by using Sentieon
• Rewrite the format of the configuration file.

Update details

• Rewrite the format of configuration file, isolated the resources option from gatk section as a new section to facilitate shared use by Sentieon and GATK.
• Added sentieon module and constructed WGS/WES analysis workflows based on sentieon.
• Removed the --max-gaussians option from the vqsr_options in the configuration file and replaced it with separate settings for SNP (vqsr_snp_max_gaussians) and Indel (vqsr_indel_max_gaussians).
• Moved the calculation of alignment statistics and data contamination section out from BQSR section to bwamem section. Changed the suffix from .recal.table to .BQSR.recal.table.
• Added the --dbsnp parameter for genotypeGVCFs to annotate known sites.
• Added fastq data filtering module based on SOAPnuke.
• Encapsulated the gatk module as a GATK class.
• Added the --interval parameter for WGS as the variant-calling-interval.
• Added a parameter to the workflow to automatically remove unnecessary sub-vcfs for WGS/WES.
• Rewrote the genotype-joint-calling module, allowing the first column of the input parameter gvcf.list to contain arbitrary interval information, including chromosome ID, chr:start-end, or a .bed file.

v1.3.2

[release v1.3.2] - 2023-05-21

Enhancements & bug fixes

v1.3.1

[release v1.3.1] - 2023-02-28

Enhancements & fixes

Bug fixs and do not delete the genomic_DB database, which has been created by the GATK genomicsDBImport process after GATK genotypeGVCFs.

v1.3.0

[release v1.3.0] - 2023-02-21

Enhancements & fixes

1. Use genomicsDBImport as a default approach to combine multi-sample gVCF files.
2. The original genotype process has been split into two steps: (1) genomicsDBImport, and (2) the final genotype joint-calling.
3. Various bugs have been fixed.
4. Added input format validation to check the validity of the input sample sheet.
5. f-string style is now used for embedding string information instead of str.format().

release v1.1.1

release version 1.1.1

version 1.0.0

Release the first version of ilus with basic functions for creating WGS/WES pipeline.

You can use this version to generate scripts for WGS/WES analysis base on the Best practice of GATK and more.