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A brief introduction to shell scripting. Please see /corral-replwork/utexasprojects/BioITeam/ngs_introcommon/scripts for several example scrtips for a number of well-written scripts.

What and why is Shell Scripting?

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login1$ ffkakldk
-bash: ffkakldk: command not found

Let’s assume that you go to a restaurant. The rule of the restaurant is to order one by one: order a drink and get it, then order an appetizer and get it, then order dishes and so forth. What a stupid ordering system is! To make matters worse, even if you want to order the exact same meal you ate before, you must go through the tedious process again. Shell scripting addresses this problem. A shell script is series of commands written in a plain text file. Instead of entering commands one by one, you can store the sequence of commands to text file and tell the shell to execute this text file. When you want to repeatedly execute the series of command lines for multiple datasets, the shell script can A shell script is series of commands written in a plain text file. Instead of entering commands one by one, you can store the sequence of commands to text file and tell the shell to execute this text file. When you want to repeatedly execute the series of command lines for multiple datasets, the shell script can automate your task and save lots of time.

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The actual bam sorting and indexing are straightforward calls to samtools (although you might want to check out the -m maximum memory option for samtools sort; it can speed up sorting of large files considerably):

echo "Sorting '$OUT_PFX.bam'...";
samtools sort $OUT_PFX.bam $OUT_PFX.sorted;
ckRes $? "samtools sort";
ckFileSz "$OUT_PFX.sorted.bam";

echo "Indexing '$OUT_PFX.sorted.bam'...";
samtools index $OUT_PFX.sorted.bam;
ckRes $? "samtools index";
ckFileSz "$OUT_PFX.sorted.bam.bai";

Finally, we call samtools flagstat to report alignment statistics:

samtools flagstat $OUT_PFX.sorted.bam | tee $OUT_PFX.flagstat.txt
ckRes $? "samtools flagstat";
ckFileSz "$OUT_PFX.flagstat.txt";

Note we tee the output so that the information is both stored in a file and appears in the execution log. Output from samtools flagstat looks like this for paired end alignments:

echo "Sorting '$OUT_PFX.bam'...";
samtools sort $OUT_PFX.bam $OUT_PFX.sorted;
ckRes $? "samtools sort";
ckFileSz "$OUT_PFX.sorted.bam";

echo "Indexing '$OUT_PFX.sorted.bam'...";
samtools index $OUT_PFX.sorted.bam;
ckRes $? "samtools index";
ckFileSz "$OUT_PFX.sorted.bam.bai";

Finally, we call samtools flagstat to report alignment statistics:

samtools flagstat $OUT_PFX.sorted.bam > $OUT_PFX.flagstat.txt
ckRes $? "samtools flagstat";
ckFileSz "$OUT_PFX.flagstat.txt";

To summarize the statistics from all your (possibly parallel) alignments, you could do something like this:

find . -name "*.flagstat.txt" | xargxargs grep 'mapped ('