Depth of Coverage v2.0

From GSA

This Walker is Deprecated

Depth of Coverage v2.0 was replaced by Depth of Coverage v3.0 in revision 3109 of the GATK

Depth of coverage

Displays the depth of coverage at all covered loci.

Reads corresponding to the intervals in the example output below

Input

Reads and reference.

Optionally allows the following arguments:

• --printBaseCounts, -bases: Print individual base counts (A,C,G,T only)
• --minMAPQ, -minMAPQ : If provided, we will also list read counts with MAPQ >= this value at a locus in coverage.
• --minDepth, -minDepth: If provided, we will also list the percentage of loci with depth >= this value per interval.
• --byReadGroup, -byRG: List read depths for each read group.
• --bySample, -bySample: List read depths for each sample.
• --printHistogram, -histogram: Print a histogram of the coverage.
• --suppressLocusPrinting, -noLocus: Don't print out locus-specific info (useful for calculating histograms)

Example

java -jar GenomeAnalysisTK.jar \
  -T DepthOfCoverage \
  -L 1:10,164,500-10,164,520\;1:10,164,550-10,164,560 \
  -R path/to/reference.fasta \
  -I path/to/input.bam

Sample Output

PER_LOCUS_COVERAGE_SECTION
location   total_coverage  coverage_without_deletions
1:10164500	4	4
1:10164501	4	4
1:10164502	5	5
1:10164503	4	4
1:10164504	3	3
1:10164505	4	4
1:10164510	7	6
1:10164511	6	6
1:10164512	6	6
1:10164513	6	6
1:10164514	6	6
1:10164515	6	6
1:10164516	6	6
1:10164517	6	6
1:10164518	6	6
1:10164519	6	6
1:10164520	6	6


PER_INTERVAL_COVERAGE_SECTION
location  total_coverage	average_coverage  coverage_without_deletions  average_coverage_without_deletions
1:10164500-10164505	24	4.00	24	4.00
1:10164510-10164520	67	6.09	66	6.00