Quality Mapping

The main module for assessing alignment quality is qualimap bamqc.

qualimap bamqc \
    -bam <input.bam> \
    -outdir <output_directory> \
    -outformat <html> \
    --java-mem-size

  • Options:

    • -bam <input.bam>: Path to the aligned BAM file (e.g., deduplicated BAM file).

    • -outdir <output_directory>: Directory for output reports.

    • -outformat <pdf|html>: Choose the output format for the report.

  • Output of Qualimap BAMQC

    The output includes:

    1. General Alignment Statistics:

      • Total number of reads.

      • Percentage of mapped reads.

      • Percentage of properly paired reads (for paired-end data).

    2. Coverage Statistics:

      • Mean coverage depth.

      • Percentage of the genome covered at varying depths (e.g., 1x, 5x, 10x).

    3. Insert Size Distribution (for paired-end reads):

      • Provides insights into library preparation and sequencing quality.

    4. GC Content Distribution:

      • Checks for bias in GC content distribution compared to expected values.

    5. Read Quality Metrics:

      • Distribution of mapping quality scores.

PreviousBismark ReportNextQC reporting

Last updated