bamfeatures

bamfeatures is a Java program for analyzing BAM files with respect to gene features defined in a GTF annotation file. It calculates read overlaps with gene and transcript features, supporting both stranded and unstranded experiments. The output summarizes various alignment features per read pair, including gene overlap counts and PCR duplicate indices.

Features

• Parses a GTF gene annotation file and a BAM alignment file.
• Classifies read pairs by overlap with genes and transcripts.
• Supports both stranded and unstranded RNA-seq data.
• Outputs summarized features for each read pair.

Usage

Requirements

• Java (JDK 8 or later)
• HTSJDK (for SAM/BAM file handling)

Command-Line Options

-gtf <file>       Path to the input GTF annotation file.
-bam <file>       Path to the input BAM file.
-o <file>         Output file path.
-frstrand [true]  (Optional) Set to 'true' for strand-specific libraries.

Example

java -cp <your_classpath> Main -gtf genes.gtf -bam sample.bam -o output.txt -frstrand true

• Replace <your_classpath> with the path to compiled classes and dependencies.
• The output file will contain a summary of features per read pair.

Notes

• The program deletes the output file if it already exists.
• For stranded protocols, specify -frstrand true; otherwise, omit the option for unstranded data.