VNtyper v1.3.0

Multiple Improvements in This Release:

• Supports processing BAM files from hg19 and hg38 alignments.
• Optimized unaligned read handling by processing them in a single pass.
• Added new argument -c or --custom_region for using other reference genomes, allowing users to specify the MUC1 gene region in their samples.
• Updated logging and error handling for better clarity.
• Introduced VNTR mean coverage calculation in the final report (New Feature).
• Removed unnecessary commented scripts.
• Improved BAM processing time, now between 5-15 minutes.

VNtyper_v1.2.0

• Small bug fixed

• Haplotype Sam file export stored in the /temp directory for visualization.

• We strongly recommend providing BAM and its index files as input to perform the genotyping faster with the Kestrel algorithm.

VNtyper v1.1.0

VNtyper v1.1.0 Release - Improved Performance

We are excited to announce the release of VNtyper v1.1.0! VNtyper is a MUC1 VNTR indel genotyper. In this latest release, we have made significant improvements to performance:

• We focused on MUC1 region instead of whole chr1 this will speed up the analysis from WES and panel data.

• We changed the --maxalignstates and --maxhapstates parameters in the Kestrel algorithm to be able to call variants with a single k-mer size = 20.

• We strongly recommend providing BAM and its index files as input to perform the genotyping faster with the Kestrel algorithm.

VNtyper_v1.0.0

VNtyper v1.0.0 Release - First release

The human genome comprises approximately 3% of tandem repeats with variable length (VNTR), a few of which have been linked to human rare diseases. Autosomal dominant tubulointerstitial kidney disease – MUC1 (ADTKD-MUC1) is caused by specific frameshift variants in the coding-VNTR of the MUC1 gene. Calling variants from VNTR using short-read sequencing (SRS) is challenging (due to poor read mappability, motif complexity, variable repetition and huge motif sequence similarities). We aimed to develop an efficient computational workflow for reliable detection of MUC1 VNTR pathogenic variants and demonstrate its clinical utility. We present herein VNtyper (VNTR genotyper), a pipeline that utilizes mapping-free genotyping using k-mer frequencies to detect small indels within MUC1-VNTR using SRS. We combined the use of our pre-built homemade MUC1-VNTR motif dictionary and a mapping-free genotyping algorithm (Kestrel) to identify and process deleterious variants.

• In this version VNtyper runs four different k-mer sizes (17,20,25, and 41) independently.
• We focused on reads aligned to chr1 and unmapped reads.
• The input file is bam and its index file.
• The final output is a single .tsv file with the pathogenic variation found.

If you have any questions, feedback or feature requests, please don't hesitate to contact us. We appreciate your support and hope you enjoy using VNtyper.

Thank you,