BAMreport

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.

If supplied with a VCF file of extermal genotypes using the "-g" option, BAMreport also includes a summary of the analysis from verifyBamID with regards to contamination estimates.

REQUIREMENTS

These tools should work on any standard 64 bit Linux environment with

• GCC
• Python (version >= 2.7.6)

INSTALLATION:

Type

git clone recursive git@github.com:aakrosh/BAMreport.git
make
make install

to install the binaries into the bin directory.

TEST DATA

The test dataset includes a BAM file and a fasta reference file. Run the tool on the dataset by running the following:

make

This should create a file "report.pdf" which should have the output similar to expected.pdf in the test_data directory.