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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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