1.SoftSearch:

 --SoftSearch is a tools that uses soft-masked reads and discordant read pairs to identify structural variation(SV) in 
   illumina next-generation sequencing data. 

 --It is a Integration of Multiple Sequence Features to Identify Breakpoints of Structural Variations.

 --Breakpoint is a place or time at which an interruption or change is made.

 --SoftSearch requires only two inputs: a BAM file of aligned reads and fasta file of the genome to which the reads were aligned.

 	
2.Setting for selecting fasta file from database.

 --Select fasta_indexes.loc file for that go to shed_tools/toolshed.g2.bx.psu.edu/repos/plus91-technologies/softsearch/
   8578d978014c/softsearch/tool-data/

 --open the fasta_indexes.loc file and make changes like

        <unique_build_id>	<dbkey>	<display_name>	<file_base_path>

        eg: hg19full	hg19	Human (Homo sapiens): hg19 Full	/depot/data2/galaxy/hg19/sam/hg19full.fa

 --open shed_tool_data_table_conf.xml file and add following.

   	<tables>
	    <table name="fasta_indexes" comment_char="#">
      	    <columns>value, dbkey, name, path</columns>
       	    <file path="/path/to/fasta_indexes.loc" />
  	    </table>
	</tables>


Notes:
  --Need latest version of Samtools(version above 0.1.18) and perl installed on local system.