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Old 12-20-2017, 09:21 AM   #1
rmf
Junior Member
 
Location: Sweden

Join Date: May 2016
Posts: 7
Smile BBMap pileup questions

I am interested in metrics that summarise coverage from my BAM file. I came across BBMap pileup which does a decent job. But I have a couple of questions.

1. It seems like if a window is provided to pileup, it returns the sum over the given window. Can other metrics such as sum/mean/median/min/max/sd/mad be calculated? I am particularly interested in the median.

2. Does pileup do only fixed windows or can it do sliding window metrics?

3. BBMap pileup returns a summary over the whole file to the console like below:

Average coverage: 71.19
Standard deviation: 198.58
Percent scaffolds with any coverage: 100.00
Percent of reference bases covered: 97.66

Can this be saved to a file? I tried '> summary.txt' at the end of my script but that didn't work.

Thanks,
Roy
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Old 12-20-2017, 11:10 AM   #2
GenoMax
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Have you tried using "out=" to save the results to a file.
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