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Notice that lines 23 and 24 are listed as unknown1 and unknown2 respectively. This information is actually While several of the other values are related to the actual library, these 2 values are actually critical to enabling and guiding the analysis (pick too small and even normal reads appear to support structural variants, pick too large and even variant reads appear as normal reads). Luckily these values are actually empirically determined as part of the preprocessing_results.txt file that was created with the perl script.

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  title Critical values and their choice
  option value reason mu_length 2223 this is taken directly from the preprocessing perl script, it enables classification of the different discordant read mappings sigma_length 1122 Again taken from the preprocessing perl script, it enables classification of the different discordant read mappings window_size 5000 Must be set to at least 2mu + (2sigma)0.5 to enable balance classification (4540 would be minimum value in this case) step_length 2500 Documentation suggest  suggests this be 25-50% of the window size, smaller sizes enable more precise endpoint determination. strand; insert size; ordering_filtering 1 Setting each to 1 turns on such filtering, absent being listed, or being listed as 0, these tests would not run You may also  consult the manual for a full description of what the commands and options inside of the svdetect.conf file.

  
  

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  title Click here for a breakdown of what this one liner is doing
  First lets break this one liner down into its 6 parts: Code Block linenumbers true mu_sigma=$(grep "^-- mu length = [0-9]*, sigma length = [0-9]*$" preprocessing_results.txt | sed -E 's/-- mu length = ([0-9]+), sigma length = ([0-9]+)/\1,\2/'); mu=$(echo $mu_sigma | cut -d "," -f 1); sigma=$(echo $mu_sigma | cut -d "," -f 2); sed -i -E "s/mu_length=unknown1/mu_length=$mu/" svdetect.conf; sed -i -E "s/sigma_length=unknown2/sigma_length=$sigma/" svdetect.conf Line 1  uses grep on the preprocessing_results.txt file looking for any line that matches "^-- mu length = [0-9]*, sigma length = [0-9]*$" and stores it in a variable mu_sigma. mu_sigma=$(......) stores everything between the () marks in a command line variable named mu_sigma ... you should notice that the closing ) mark is actually on line 2 the | at the end of the line is the "pipe" command which passes the output to the next command (line in this case as we have broken the command up into parts) Line 2 uses the sed command to delete everything that is not a number or , and finishes storing the output in the mu_sigma variable sed commands can be broken down as follows: 's/find/replace/' in this case, find: -- mu length = ([0-9]+), sigma length = ([0-9]+) where : [0-9] is any number the + sign means find whatever is to the left 1 or more times and things between () should be remembered for use in the replace portion of the command likewise, in this case, replace: \1,\2/ where \1 means whatever was between the first set of () marks in the find portion , is a literal comma \2 means whatever was between the sescond set of () marks in the find portion at the end of line 2 we now have a new variable named mu_sigma with a value of "2223,1122" Line 3 creates a new variable named mu and gives it the value of whatever is to the left of the first , it finds. echo $mu_sigma | pass the value of $mu_sigma to whatever is on the other side of | cut -d "," -f 1 divide whatever the cut command sees at all the "," marks and then print whatever is to the left of the 1st   at the end of line 3 we now have a variable named mu with the value "2223" Line 4 does the same thing as line 3 except for a variable named sigma, and takes whatever is between the 2nd comma and 3rd comma (since we only have 1 comma, its taking whatever comes after the comma) at the end of line 4 we now have a variable named sigma with the value "1122" Line 5 looks through the entire svdetect.conf file looking for a line that matches mu_length=unknown1 and replaces all that text with mu_length=$mu (except the computer knows $mu is the variable with the value 2223. the -i option tells the sed command to do the replacement in place meaning you are changing the contents of the file the "" marks tell the command line that you want to evaluate whatever is between the ""marks, in this case, the mu variable at the end of line 5, our svdetect.conf file line 23 now reads mu_length=2223 Line 5 looks through the entire svdetect.conf file looking for a line that matches sigma_length=unknown2 and replaces all that text with sigma_length=$sigma (except the computer knows $sigma is the variable with the value 1122. the -i option tells the sed command to do the replacement in place meaning you are changing the contents of the file the "" marks tell the command line that you want to evaluate whatever is between the ""marks, in this case, the sigma variable at the end of line 5, our svdetect.conf file line 24 now reads sigma_length=1122

  
  

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I've copied a few of the lines after pasting into excel below :

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