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

  • DumpSTR filters VCF files with TR genotypes, performing call-level and locus-level filtering, and outputs a filtered VCF file.

StatSTR

  • StatSTR takes in a TR genotyping VCF file and outputs per-locus statistics.

qcSTR

  • qcSTR generates plots that are useful for diagnosing issues in TR calling.

CompareSTR

  • 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

  • MergeSTR merges multiple VCF files produced by the same TR genotyper into a single VCF file.