What it does
This tool identifies simple as well interrupted STRs. Choosing a hamming distance of zero will return simple STRs. Choosing a hamming distance of greater than zero will return both simple and interrupted STRs. The algorithms used to identify simple and interrupted STRs are described oin the manuscript cited below (see TABLE XXXX).
Citation
When you use this tool, please cite Fungtammasan A, Ananda G, Hile SE, Su MS, Sun C, Harris R, Medvedev P, Eckert K, Makova KD. 2015. Accurate Typing of Short Tandem Repeats from Genome-wide Sequencing Data and its Applications, Genome Research This tool is developed by Chen Sun (cxs1031@cse.psu.edu) and Bob Harris (rsharris@bx.psu.edu)
Input
Output
For fastq, the output will contain the following columns:
For fasta, fastq without quality score and sam format, column 8 will be replaced with dot(.).
If the users have mapped file (SAM) and would like to profile STRs from premapped data instead of using flank-based mapping approach, they can select SAM format input and specify that they want correspond STRs in reference for comparison. The output will be as follow: