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rmf 12-20-2017 09:21 AM

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.


GenoMax 12-20-2017 11:10 AM

Have you tried using "out=" to save the results to a file.

silask 06-04-2018 12:28 AM


I assembled metagenomic reads and want to know how many reads are mapping to the contigs.

I created a sam file using bbwrap for paired-end libraries with singletons. So the sam files consist of paired and unpared reads.

The log file of bbwrap shows me that for different samples reads are mapped usually 40-70% of the paired and 30-50% of the singeltons. However, the pileup log files say that in all samples 48-49% of reads were mapped. This makes no sense to me.

I used v 37.78 and activated physical coverage.
Can pileup not handle paired end + singletons in the same file?

it seems that it's due to the physical cov.

silask 06-06-2018 05:28 AM

There is still something strange.

in the log file of bbwrap I have


* | Paired end | Se
-- | -- | --
Total reads | 2 x 16895000 | 31401969
mapped | 2x 13408609 | 29907540
* | * | *
mapped | 79% | 95%

Which seem to be correct. e.g. the number of unmapped reads are found in `outu`

in the logfile of pilup it is written:

Reads: | 27370533
-- | --
Mapped reads: | 26817218
Mapped bases: | 4022582700
Ref scaffolds: | 851270
Ref bases: | 1216084673
* | *
Percent mapped: | 97.978
Percent proper pairs: | 97.978

I have no Idea, how pilup finds only 27370533 reads.

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