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SVDetect demonstrates a common strategy in some programs with complex input where instead of including a lot of options on the command line, it reads in a simple text file that sets all of the required options. Lets look at how to create a configuration file:
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You'll need to substitute your own paths for /full/path/to/61FTVAAXX.ab.sam and /full/path/to/NC_012967.1.lengths on lines 7 and 8 below. |
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<general> input_format=sam sv_type=all mates_orientation=RF read1_length=35 read2_length=35 mates_file=/full/path/to/61FTVAAXX.ab.sam cmap_file=/full/path/to/NC_012967.1.lengths num_threads=1 </general> <detection> split_mate_file=0 window_size=2000 step_length=1000 </detection> <filtering> split_link_file=0 nb_pairs_threshold=3 strand_filtering=1 </filtering> <bed> <colorcode> 255,0,0=1,4 0,255,0=5,10 0,0,255=11,100000 </colorcode> </bed> | ||||
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You also need to create a tab-delimited file of chromosome lengths. Use the tab key rather than writing out <tab>!!
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You'll want to submit the first two commands to the TACC queue or do them in an idev
shell. They take a while.Consult Consult the manual for a full description of what these commands and options are doing while the commands are running.
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SVDetect linking -conf svdetect.conf SVDetect filtering -conf svdetect.conf SVDetect links2SV -conf svdetect.conf |
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