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The which command is used to give the location of a program or script that is in your $PATH.
This script simply does a format conversion and then calls
change name of code block
This script is written in perl (a programing language that while powerful, is not very favored among most computational biologists who typically prefer: Python, R, or Bash shell scripts) as a method of standardizing input to call a series of external commands. Such wrappers (or wrappers within wrappers) make your life much easier. breseq itself has wrappers for using bowtie2 and samtools which you ran separately on other data. As you increase your understanding of scripts and the command line by looking at what others have done you may begin to make your own wrappers and small scripts, but such wrappers are a great example of the BioITeam and other community resources can provide you with. While we have told you no one will ever care as much about your data as you do, quality of life issues regarding repetitive treatment of similar inputs and outputs may be easily solved by someone else. |
Now let's run it on the .vcf files from the 3 individuals (NA12878, NA12891, and NA12892) from both the samtools and gatk output in the $BI/ngs_course/human_variation/ directory. (You may recognize these as the same individuals that we worked with on the Trios tutorial. Throughout the class we've been teaching you how to create a commands file using nano, but here we provide a more complex example of how you can generate a commands file. As you become more proficient with the command line, it is likely you will use various piping techniques to generate commands file. The following calls Perl to custom-create the 6 command lines needed and put them straight into a commands file:
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ls $BI/ngs_course/human_variation/N*.vcf | \ perl -n -e 'chomp; $_=~/(NA\d+).*(sam|GATK)/; print "annovar_pipe.sh $_ >$1.$2.log 2>&1\n";' > commands |
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cds
mkdir BDIB_Annovar
cd BDIB_Annovar
# Use only 1 of the following copy commands
# if you have already done the trios tutorial
cp $SCRATCH/BDIB_Human_tutorial/raw_files/N*.vcf .
# if you have not done the trios tutorial
cp $BI/ngs_course/human_variation/N*.vcf .
ls *.vcf | perl -n -e 'chomp; $_=~/(NA\d+).*(sam|GATK)/; print "annovar_pipe.sh $_ >$1.$2.log 2>&1 &\n";' > commands
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| "commands" files are 1 way to both create a record of what it is that you are doing as well as an easy way to execute multiple commands simultaneously. In a previous tutorial (the advanced breseq tutorial, or the 2nd breseq example from the first day) we showed you how to do this by adding an & as the last character of the line to force the command to execute in the background. Tomorrow we will go over the more common method of submitting "commands" files to the que to run as jobs rather than being spoiled with interacting with everything on idev nodes. In computational biology this instructor has often found that once I learn to do something a particular way, it takes an incredible amount of inertia to change how I do something even when i know it would help to do so. In an effort to learn from me |
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make me an expand
investigate the commands file to to determine what the piping command actually did (click for answer)
make me a code block
cat commands
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| making things harder on myself than need be, I urge you to STRONGLY consider not naming every list of commands you want to run "commands" but rather something that is actually descriptive, even "commands_DATE" would be helpful. As you start submitting your own jobs you will quickly be able to build bad habits, try to be aware of and avoid this one if possible. |
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The easiest way to check if this is working is to use ls and see an explosion of new files. This will take quite a bit of time to complete running. As such, we have ALREADY pre-computed these outputs so you can begin evaluating the results.
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cds mkdir BDIB_Annovar cd BDIB_Annovar cp $SCRATCH/BDIB_Human_tutorial/raw_files/N*.vcf . ls *.vcf | perl -n -e 'chomp; $_=~/(NA\d+).*(sam|GATK)/; print "annovar_pipe.sh $_ >$1.$2.log 2>&1 &\n";' > commands |
change title of codeblock = MAKE SURE YOU ARE ON IDEV if you want to run
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chmod +x commands
./commands |
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mkdir provided_results
cd provided_results
cp $BI/ngs_course/human_variation/*chrom20.samtools* . |
Later, when your results have completed running (likely >90 minutes as annovar not configured to use multiple processes, compare your results to these provided results).
For the scavengar hunts below you should also copy over the GATK results.
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cp $BI/ngs_course/human_variation/*chrom20.GATK* . |
ANNOVAR output
Annovar does a ton of work in assessing variants for us (though if you were going for clinical interpretation, you still have a long way to go - compare this to RUNES or CarpeNovo). It provides all these output files:
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