Supplementary Figure 3: Comparison of accuracy of sequence-alignment tools at MS loci.
From: Analysis of somatic microsatellite indels identifies driver events in human tumors
Noise is plotted as a function of the MS repeat length for the standard alignment (using Burrows-Wheeler Aligner, BWA2) versus the MS-specific alignment (adapted from lobSTR3). Data is shown for the AG motif. Noise was defined as the fraction of reads that differ from the modal number of repeats, aggregated over all the MS loci in the X-chromosome from normal male samples (which are assumed to be homozygous at each MS locus). On average, noise is reduced by approximately a factor of 5 using the MS-specific alignment method.
2. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinforma. Oxf. Engl. 25, 1754–1760 (2009).
3. Gymrek, M., Golan, D., Rosset, S. & Erlich, Y. lobSTR: A short tandem repeat profiler for personal genomes. Genome Res. 22, 1154–1162 (2012).
