Fig 1.
Flowchart of analyses and samples used in this study.
a) Genome in a bottle (GIAB) samples. b) 1000 Genomes project samples. c) Known clinical samples available from Coriell.
Table 1.
Software for genotyping tandem repeats compared.
Table 2.
Samples used in this study.
Table 3.
Comparison of processing times and memory usage of STR-calling software.
Fig 2.
Comparison of STR calls from ExpansionHunter, HipSTR and GangSTR.
A). Comparison of the HG002 genotypes of the STRs called by both GangSTR and HipSTR. The x -axis represents the call made by GangSTR in comparison to the reference sequence (0 = same as reference sequence, -100 represents 100 fewer repeat units than the reference sequence. The y-axis represents the call made by HipSTR. B) Comparison of the genotypes of the STRs called by either GangSTR or HipSTR compared to ExpansionHunter (x-axis). The dotted red lines shows correlation between the calls compared.
Table 4.
Percentage of loci called in a shared STR catalogue by GangSTR and HipSTR and ExpansionHunter.
Table 5.
Mendelian inheritance of STR alleles.
Fig 3.
Repeat unit size distribution of Mendelian inconsistencies.
a) ExpansionHunter, GangSTR and HipSTR calls that are Mendelian inconsistent as a proportion of motif counts in the catalogue, b) all STRs in the catalogue used by the three software tools.
Table 6.
Comparison of STR genotype calls at core forensic loci for NA12878.
Table 7.
Detection of STR expansions at known clinical loci.