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. 2021 May 5;37(5):731-733.
doi: 10.1093/bioinformatics/btaa736.

TRTools: a toolkit for genome-wide analysis of tandem repeats

Nima Mousavi  1 , Jonathan Margoliash  2 , Neha Pusarla  3 , Shubham Saini  4 , Richard Yanicky  2 , Melissa Gymrek  2   4
Affiliations

TRTools: a toolkit for genome-wide analysis of tandem repeats

Nima Mousavi et al. Bioinformatics. .

Abstract

Summary: A rich set of tools have recently been developed for performing genome-wide genotyping of tandem repeats (TRs). However, standardized tools for downstream analysis of these results are lacking. To facilitate TR analysis applications, we present TRTools, a Python library and suite of command line tools for filtering, merging and quality control of TR genotype files. TRTools utilizes an internal harmonization module, making it compatible with outputs from a wide range of TR genotypers.

Availability and implementation: TRTools is freely available at https://github.com/gymreklab/TRTools. Detailed documentation is available at https://trtools.readthedocs.io.

Supplementary information: Supplementary data are available at Bioinformatics online.

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Figures

Fig. 1.
Fig. 1.
TRTools visualizations. (a) Allele frequency distribution at an example pentanucleotide TR output by statSTR based on GangSTR genotypes for two sample sets (YRI population consisting of Yorubans from Nigeria and CEU population of Northwestern European descent). (b) Example TR genotype comparison output by compareSTR. The plot compares genotypes (in terms of number of repeats difference from hg19) from HipSTR (x-axis) to those from ExpansionHunter (y-axis) on 5000 tetranucleotide TRs. Bubble sizes give the number of calls included in each point. (c) Example reference bias plot output by qcSTR using popSTR2 genotypes. The plot shows the average deviation of TR alleles called versus the reference length of the TR (in bp). The red line shows the cumulative percentage of allele calls below each reference length threshold
See this image and copyright information in PMC

References

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