Command-Line Tools

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.