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<tool id="microsatpurity" name="Select uninterrupted STRs" version="1.0.0">
  <description> of a specific column</description>
  <command interpreter="python">microsatpurity.py $input $period $column_n > $output </command>

  <inputs>
    <param name="input" type="data" label="Select input" />
    <param name="period" type="integer" label="motif size" value="1"/>
    <param name="column_n" type="integer" value="0" label="Select column that contains microsatellites of interest (0 = last column)" />
  </inputs>
  <outputs>
    <data format="tabular" name="output" />
    
  </outputs>
  <tests>
    <!-- Test data with valid values -->
    <test>
      <param name="input" value="microsatpurity_in.txt"/>
      <param name="period" value="2"/>      
      <param name="column_n" value="0"/>
      <output name="output" file="microsatpurity_out.txt"/>
    </test>
    
  </tests>
  <help>


.. class:: infomark

**What it does**

This tool is used to select only the uninterrupted STRs/microsatellites. Interrupted STRs (e.g. ATATATATAATATAT) or sequences of STRs with non-STR parts (e.g. ATATATATATG) will be removed.

As another application of this tool, specifically for STR-FM pipeline (profiling STRs in short read data), it can be used to avoid the cases where flanking bases were misread as STRs (sequencing errors). Thus, the remaining read profile will only reflect the variation of TR length from expansion/contraction.
For example, suppose that the sequence around an STR in the reference genome is AGCGACGaaaaaaGCGATCA. If we observe a read with sequence AGCGACGaaaaaaaaaaGCGATCA, we can indicate that this is an STR expansion. However, if we observe another read with sequence AGCGACGaaaaaaaCGATCA, this is likely a substitution of G to A. Such incidents can be removed with this tool.
You can use the tool **combine mapped flanking bases** to get the STRs in reference that correspond to sequence between mapped reads. If the user map these reads around the uninterrupted STRs in reference, the corresponding sequences between these pairs should be the uninterrupted STRs regardless of expansion/contraction of STRs in short read data. However, if the substitution of flanking base or if the fluorescent signal from the previous run make it look like substitution, the corresponding sequences in reference in between the pairs will not be uninterrupted STRs. Thus this tool can remove those cases and keep only STR expansion/contraction.


**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 for STRs profiling, it should contains:

- Column 1 = STR location in reference chromosome
- Column 2 = STR location in reference start
- Column 3 = STR location in reference stop
- Column 4 = STR location in reference motif
- Column 5 = STR location in reference length
- Column 6 = STR location in reference motif size
- Column 7 = length of STR (bp)
- Column 8 = length of left flanking region (bp)
- Column 9 = length of right flanking region (bp)
- Column 10 = repeat motif (bp)
- Column 11 = hamming distance 
- Column 12 = read name
- Column 13 = read sequence with soft masking of STR
- Column 14 = read quality (the same Phred score scale as input)
- Column 15 = read name (The same as column 12)
- Column 16 = chromosome 
- Column 17 = left flanking region start
- Column 18 = left flanking region stop
- Column 19 = STR start as infer from pair-end
- Column 20 = STR stop as infer from pair-end
- Column 21 = right flanking region start
- Column 22 = right flanking region stop
- Column 23 = STR length in reference
- Column 24 = STR sequence in reference

**Output**

The same as input format.


</help>
</tool>