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
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