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Old 06-21-2011, 03:13 PM   #1
CNVboy
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Location: boston

Join Date: Jun 2011
Posts: 27
Default About script to combine steps of BWA

For BWA, first do alignment (generate .sai), then sampe the paired-ends (generate .sam), then convert .sam to .bam. Now I'm going to write script to combine all these steps. ie, input is fastq, then output is .bam file.

Now a big question is, I need to guarantee, say, the first step (generating .sai) is COMPLETE (instead of being aborted) before going to the second step; and the second step (generating .sam) before the third. I there any way to check that for BWA? Or what's the sign for the completeness of each step?

btw, for combining of steps of BWA, I just need to put those three commands together? Or any other trick?

thanks!
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