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.

AssociaTR

• associaTR performs association testing of the lengths of TRs against phenotypes.

PrancSTR

• prancSTR quantifies evidence of somatic mosaicism at STRs using VCF files generated by HipSTR.

SimTR

• SimTR simulates next generation sequencing reads at a single TR region while modeling stutter errors common in such sequencing.

annotaTR

• AnnotaTR takes in a TR genotype VCF file and outputs a new file (VCF or PGEN) with additional INFO/FORMAT fields