Additional file 2 of Genome-wide sequencing as a first-tier screening test for short tandem repeat expansions

Additional file 2: Table S3: CAUSES exome sequence data summary. Table S4: Commands and parameters used for the implementation of lobSTR, RepeatSeq, HipSTR, TREDPARSE, ExpansionHunter, STRetch, exSTRa, and GangSTR. Table S5: Summary of repeat loci in catalogs used by short tandem repeat analysis methods. Table S6: Short tandem repeat calls of ExpansionHunter, GangSTR, TREDPARSE, lobSTR, HipSTR, RepeatSeq, STRetch, and exSTRa in the Isaac-aligned European Genome-phenome Archive and simulated genomes. Table S7: Short tandem repeat calls of ExpansionHunter, GangSTR, TREDPARSE, lobSTR, HipSTR, RepeatSeq, STRetch, and exSTRa in the BWA-aligned European Genome-phenome Archive and simulated genomes. Table S8: Known normal alleles characterised by ExpansionHunter, GangSTR, TREDPARSE, lobSTR, HipSTR, and RepeatSeq in the European Genome-phenome Archive and simulated genomes. Table S9: Known FMR1 intermediate and premutation alleles characterised by ExpansionHunter, GangSTR, TREDPARSE, lobSTR, HipSTR, and RepeatSeq in the European Genome-phenome Archive and simulated genomes. Table S10: Full-mutation alleles characterised by ExpansionHunter, GangSTR, and TREDPARSE in the European Genome-phenome Archive and simulated genomes. Table S11: Performance of short tandem repeat callers on simulated and real genomes with FMR1 CGG-repeat expansions in normal, premutation, and full-mutation size ranges. Table S12: Analysis and detection of DMPK, FMR1, and FXN full-mutation alleles using ExpansionHunter version 2 and GangSTR with and without off-target sites. Table S13: ExpansionHunter, STRetch, and exSTRa calls and molecular validation results of the short tandem repeat candidates identified in the CAUSES and IMAGINE genomes and exomes. Table S14: Repeat length distributions of the genotyped AR, ATN1, ATXN1, ATXN2, ATXN3, ATXN7, ATXN8/ATXN8OS, ATXN10, C9orf72, CACNA1A, CBL, CNBP, CSTB, DMPK, FMR1, FMR2, FXN, HTT, JPH3, NOP56, PHOX2B, PPP2R2B, and TBP alleles in the CAUSES and IMAGINE genomes. Table S15: Summary of performance metrics of the best model and individual STR tools in BWA modified analysis. Table S16: Run-time and peak memory requirements of short tandem repeat callers and aligners on a 40x human genome.