vclust

A tool to detect variation clusters in PacBio HiFi sequencing data

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Variation clusters are loosely defined as contiguous regions that contain some variation in a given set of genomes. The vclust method is designed to locate variation clusters around an input set of seed regions using variation extracted from PacBio HiFi whole-genome sequencing data.

Authors: Egor Dolzhenko

Installation and usage

vclust can be built from source (requires Rust, which can be installed with the rustup tool).

git clone git@github.com:PacificBiosciences/vclust.git
cd vclust
cargo build --release

Once installed, vclust can be run like so:

./vclust --genome genome.fa --reads bams/*.bam --regions regions.bed > extended_regions.txt

where

• genome.fa is the reference genome (the same reference genome as used for read alignment)
• bams/*.bam paths to the aligned PacBio HiFi BAM files
• regions.bed a BED file with seed regions to extend
• extended_regions.txt an output file with the extended regions

The input file regions.bed is expected to contain coordinates and identifiers of the regions to be profiled.

chr1    57367043        57367119        region1
chr1    146228800       146228821       region2
chr1    149390802       149390841       region3
chr10   79826383        79826404        region4
chr10   93702522        93702547        region5
chr11   66744821        66744850        region6
chr11   119206289       119206322       region7

The output file extended_regions.txt contains region identifiers (column 1), coordinates of the original input regions (column 2), input regions' start / end extension lengths (columns 3,4), and coordinates of the corresponding extended regions (column 5). If vclust is unable to extend a given region (due to, say, the lack of read coverage), the third column is set to NA.

region1 chr1:57367043-57367119      0    0       chr1:57367043-57367119
region2 chr1:146228800-146228821   NA
region3 chr1:149390802-149390841    0    0       chr1:149390802-149390841
region4 chr10:79826383-79826404    72    0       chr10:79826311-79826404
region5 chr10:93702522-93702547     0    0       chr10:93702522-93702547
region6 chr11:66744821-66744850     0    0       chr11:66744821-66744850
region7 chr11:119206289-119206322   0    0       chr11:119206289-119206322

In the example above, vclust did not identify significant variation around region1 and hence the extension lengths were set to 0. The reported extended region in column 5 is the original region itself. On the other hand, the start of region4 was extended by 72 bps, expanding coordinates of the original region from chr10:79826383-79826404 to chr10:79826311-79826404.

Citation

vclust is described in the Methods section of this paper:

Ben Weisburd, Egor Dolzhenko, Mark F. Bennett, Matt C. Danzi, Adam English, Laurel Hiatt, Hope Tanudisastro, Nehir Edibe Kurtas, Helyaneh Ziaei Jam, Harrison Brand, Fritz J. Sedlazeck, Melissa Gymrek, Harriet Dashnow, Michael A. Eberle, Heidi L. Rehm. Defining a tandem repeat catalog and variation clusters for genome-wide analyses and population databases. bioRxiv, 2024-10.

Need help?

If you notice any missing features, bugs, or need assistance with analyzing the output of vclust, please don't hesitate to open a GitHub issue or contact the developers by email.

vclust is a pre-release software intended for research use only and not for use in diagnostic procedures. While efforts have been made to ensure that vclust lives up to the quality that PacBio strives for, we make no warranty regarding this software.

As vclust is not covered by any service level agreement or the like, please do not contact a PacBio Field Applications Scientists or PacBio Customer Service for assistance with any vclust release. Please report all issues through GitHub instead. We make no warranty that any such issue will be addressed, to any extent or within any time frame.

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