TRTools offers a variety of command-line tools for performing manipulations to TR genotype VCFs. (These tools have ‘STR’ in their name, but are applicable to all TR VCFs).
DumpSTR filters VCF files with TR genotypes, performing call-level and locus-level filtering, and outputs a filtered VCF file.
StatSTR takes in a TR genotyping VCF file and outputs per-locus statistics.
qcSTR generates plots that are useful for diagnosing issues in TR calling.
CompareSTR compares different TR callsets generated on the same samples against the same reference panel. CompareSTR outputs overall, per-locus, and per-sample concordance information.
MergeSTR merges multiple VCF files produced by the same TR genotyper into a single VCF file.
associaTR performs association testing of the lengths of TRs against phenotypes.
prancSTR quantifies evidence of somatic mosaicism at STRs using VCF files generated by HipSTR.
SimTR simulates next generation sequencing reads at a single TR region while modeling stutter errors common in such sequencing.