What it does

• This tool will take SAM file (sorted by read name), remove unpaired reads, and combine paired faux read-pairs into a single row. It also reports Short Tandem Repeats (STRs) sequences in the reference genome that correspond to the space between the faux paired end reads and the coordinate of start and stop for left and right flanking regions of STRs.

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

• Sorted SAM files by read name.

Output

The output will combine the two faux paired-end read lines of input ito the following single line format:

• Column 1 = read name
• Column 2 = chromosome
• Column 3 = left flanking region start
• Column 4 = left flanking region stop
• Column 5 = STR start
• Column 6 = STR stop
• Column 7 = right flanking region start
• Column 8 = right flanking region stop
• Column 9 = STR length in reference
• Column 10= STR sequence in reference