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This next exercise will give you some idea of how Annovar works; we've taken the liberty of writing the bash script annovar_pipe.sh
around the existing summarize_annovar.pl
wrapper (a wrapper within a wrapper - a common trick) to even further simplify the process for this course.
Running Annovar
Get some data:
First we want to move to a new location on $SCRATCH
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Note that the above block does not include how to make the edits, nor the saving and closing of the slurm file. The needed edits are:
Line number | As is | To be |
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16 | #SBATCH -J jobName | #SBATCH -J spades |
17 | #SBATCH -n 1 | #SBATCH -n 6 |
22 | ##SBATCH --mail-user=ADD | #SBATCH --mail-user=<YourEmailAddress> |
23 | ##SBATCH --mail-type=all | #SBATCH --mail-type=all |
29 | export LAUNCHER_JOB_FILE=commands | export LAUNCHER_JOB_FILE=annovar_commands |
The changes to lines 22 and 23 are optional but will give you an idea of what types of email you could expect from TACC if you choose to use these options. Just be sure to pay attention to these 2 lines starting with a single # symbol after editing them.
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Again use ctl-o and ctl-x to save the file and exit.
Analyzing the results
Accessing pre-computed results
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Everything after the "LJB_GERP++" field in exome_summary came from the original VCF file, so this file REALLY contains everything you need to go on to functional analysis! This is one of the many reasons I like Annovar.
Scavenger hunts! and command line building
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The final answer is "DEFB126"
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