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Table 1 Execution time comparison of MutScan and conventional pipelines

From: MutScan: fast detection and visualization of target mutations by scanning FASTQ data

Sample ID Base number GATK pipeline called variants Tumor pipeline called variants GATK pipeline time Tumor pipeline time MutScan time (GATK VCF) MutScan time (tumor pipeline VCF) MutScan time (built-in mutation)
S001 3.07 G 376 1163 166m01s 84m26s 3m09s 4m31s 1m28s
S002 2.70 G 376 1438 158m40s 64m09s 3m03s 4m50s 1m11s
S003 4.98 G 531 949 236m57s 135m47s 4m57s 6m59s 2m19s
S004 3.51 G 375 798 186m48s 100m14s 3m16s 4m26s 1 m 34 s
S005 3.50 G 385 751 191m29s 84m24s 3m26s 4m20s 1m34s
S006 3.67 G 359 1303 182m42s 96m50s 3m24s 5m57s 1m36s
S007 6.08 G 380 2055 200m22s 142m30s 4m20s 11m17s 2m29s
S008 3.33 G 383 873 175m16s 90m27s 2m52s 4m37s 1m20s
  1. The input files are Gzip compressed paired-end sequencing FASTQ, and the base number is the summation of both paired files. Since the tumor and GATK pipeline used different variant detection and filtering strategies, the tumor pipeline detected more variants than the GATK pipeline. The column MutScan (GATK VCF) is the execution time of MutScan for processing time with the VCF (INDEL + SNV) called by the GATK pipeline, similarly for the column MutScan (tumor pipeline VCF). When MutScan was ran with a VCF, its execution time was predominantly determined by the size of the FASTQ file and the number of variants