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.