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

BMC Bioinformatics

Table 1 Execution time comparison of MutScan and conventional pipelines

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

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

ISSN: 1471-2105