BIONODE Open Access Tools

Function:

samtools depth is a command-line tool used to calculate sequencing depth (coverage) at each genomic position from SAM, BAM, or CRAM alignment files. It reports the number of reads covering every position in the reference genome and is widely used for coverage assessment and quality control in sequencing experiments.

Input Format:

• SAM (Sequence Alignment/Map) file
• BAM (Binary Alignment/Map) file
• CRAM (Compressed Reference-oriented Alignment Map) file

Output Format:

• Tab-delimited text file containing:
  • Reference sequence name
  • Genomic position
  • Read depth (coverage)

Example Output:

chr1    100    30
chr1    101    31
chr1    102    32
chr1    103    29

This indicates that position 100 on chromosome 1 is covered by 30 reads, position 101 by 31 reads, and so on.

Applications:

• Coverage analysis for sequencing experiments.
• Quality control of alignment files.
• Identification of low-coverage genomic regions.
• Validation of targeted sequencing panels.
• Copy number variation and coverage-based studies.
• Preparation of depth information for downstream analysis.

Suggested Reading:

Official Samtools Manual Pages: Samtools Depth Manual

Citation:

If you use samtools depth in your work, please cite the following reference:

Li, H., Handsaker, B., Wysoker, A., et al. (2009). The Sequence Alignment/Map (SAM) format and SAMtools. Bioinformatics, 25(16), 2078-2079. doi:10.1093/bioinformatics/btp352