What it does
This tool is used to select only those input lines that have compatible STR motifs between the two user-specified columns. Two STR motifs are called compatible if they are either identical, or complementary, or produce the same sequence on rotating the start of the motif. For example, A is considered compatible with A and its reverse complement T. Similarly, AGG considered compatible with AGG, its reverse complement TCC, and their rotations GGA, GAG, CCT and CTC.
For STR-FM pipeline (profiling STRs in short read data), this tool can be used to make sure that the STRs in the reads have the compatible motif as the STRs in the reference at the corresponding mapped location.
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
Input
The input files can be any tab delimited file.
If this tool is used in STR-FM pipeline for STRs profiling, it should contains:
Output
The same as input format.