Report on a BAM file.
BAMreport creates a PDF report (which can be user specified) and puts all the QC graphs and plots in it. The output file includes the following:
- Alignment statistics from the BAM file.
- Nucleotide composition on both reads of fragment as the position on sequence is varied.
- Base quality variation with position on sequence.
- Depth of coverage distribution.
- Relative depth of coverage distribution based on the specified window size.
- Variation of GC and coverage.
- Insert length distribution.
- Variation of read lengths.
- Frequency of clipping on the 5' end which is indicative of adapters or other contaminations.
- Mismatches on the reads against the reference and their variation with position.
- Indels on the reads against the reference and their variation with position on the reads.
These tools should work on any standard 64 bit Linux environment with
- GCC
- Python (version >= 2.7.6)
- R & Rscript
- MASS
- ggplot2
- RColorBrewer
The test dataset includes a BAM file and a fasta reference file. Run the tool on the dataset by running the following:
./../src/BAMreport -w 100 reference.fa alignments.bam
This should create a file "report.pdf" which should have the output similar to expected.pdf in the test_data directory.