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Inspecting bam files for quality. Comes from same home as Blast2Go, the famous functional annotation system, in CIPF, Valencia, Spain.


Has a number of dependencies:

  • optparse (available from CRAN)
  • NOISeq, Repitools, Rsamtools, GenomicFeatures, rtracklayer (available from Bioconductor)


On its own, the GUI will be launched.

However if you launch

qualimap bamqc -bam <bamfile> -outfile <youpdfname.pdf>

it seems to know it should behave in command-line fashion

Typical output (truncated)
Processed 400 out of 403 windows...
Total processed windows:403
Number of reads: 790595
Number of valid reads: 72116
Number of correct strand reads:0

Inside of regions...
Num mapped reads: 72116
Num mapped first of pair: 36084
Num mapped second of pair: 36032
Num singletons: 1216
Time taken to analyze reads: 159
Computing descriptors...
numberOfMappedBases: 14882078
referenceSize: 3359974
numberOfSequencedBases: 14876535
numberOfAs: 4618823
Computing per chromosome statistics...
Computing histograms...
Overall analysis time: 160
end of bam qc
Computing report...
Writing PDF report...
PDF file created successfully

If you used the -outfile option, It creates a directory where is will put a pdf file, and a txt file. The name of the directory is usualy the root name of the bamfile.