--genome <GENOME>Path to the FASTA file containing reference genome. This must be the same reference genomes as the one used for read alignment.--reads <READS>BAM file with alignments of HiFi reads.--repeats <REPEATS>BED file with reference coordinates and structure of tandem repeats.--output-prefix <OUTPUT_PREFIX>Prefix for output files. TRGT generates an unsorted VCF file (<OUTPUT_PREFIX>.vcf.gz) and unsorted BAM file with pieces of HiFi reads overlapping the repeats (<OUTPUT_PREFIX>.spanning.bam).--threads <THREADS>Number of threads. Set to 1 by default.
--genome <GENOME>Path to the FASTA file containing reference genome.--repeats <REPEATS>BED file with repeat coordinates and structure.--spanning-reads <SPANNING_READS>BAM file generated by TRGT.--vcf <VCF>VCF file generated by TRGT.--repeat-id <REPEAT_ID>ID of the repeat to visualize.--plot-type <plot type>TRVZ can generate two types of plots: allele plots and waterfall plots. Allele plots show alignments of reads to each repeat allele. Waterfall plots display unaligned repeat sequences without aligning them to the (consensus) allele. Waterfall plots are especially useful for QC of repeat calls and for visualization of mosaic expansions. TRVZ generates allele plots by default.--show <show>TRVZ can either visualize motifs (motifs) or methylation (meth). Motifs are visualized by default.--image <OUTPUT_PATH>Output image path with ends with extension .pdf, .svg, or .png.