Coverage Report

The cov_report report generates a _cov_report.bed file in a tab-delimited format. The first three columns are standard BED fields. The DRAGEN Amplicon pipeline includes a fourth column for name and fifth column for gene_id. The remaining column fields are statistics calculated over the interval region specified on the same record line.

The following table lists the appended columns.

Column

Description

total_cvg

The total coverage value.

mean_cvg

The mean coverage value.

Q1_cv

The lower quartile (25th percentile) coverage value.

median_cvg

The median coverage value.

Q3_cvg

The upper quartile (75th percentile) coverage value.

min_cvg

The minimum coverage value.

max_cvg

The maximum coverage value.

pct_above_X

Indicates the percentage of bases over the specified interval region that had a depth coverage greater than X.

By default, if an interval has a total coverage of 0, then the record is written to the output file. To filter out intervals with zero coverage, set vc-emit-zero-coverage-intervals to false in the configuration file.

The following is an example of the contents of the _cov_report.bed file:

chrom  start      end        total_cvg  mean_cvg  Q1_cvg  median_cvg  Q3_cvg  min_cvg  max_cvg  pct_above_5 …
chr5   34190121   34191570   76636      52.89     44.00   54.00       60.00   32       76       100.00      …
chr5   34191751   34192380   39994      63.58     57.00   61.00       69.00   50       85       100.00      …
chr5   34192440   34192642   10074      49.87     47.00   49.00       51.00   44       62       100.00      …
chr9   66456991   66457682   31926      46.20     39.00   45.00       52.00   27       65       100.00      …
chr9   68426500   68426601   4870       48.22     42.00   48.00       54.00   39       58       100.00      …
chr17  41465818   41466180   24470      67.60     4.00    66.00       124.00  2        153      66.30       …
chr20  29652081   29652203   5738       47.03     40.00   49.00       52.00   34       58       100.00      …
chr21  9826182    9826283    4160       41.19     23.00   52.00       58.00   5        60       99.01       …

The following table shows which outputs are generated when default options (--vc-target-bed) versus optional coverage region options (--coverage-region) are used.

--vc-target-bed specified? Y/N

--qc- coverage-region-i (i equal to 1, 2, or 3) specified? Y/N

Expected Output Files

N

N

wgs_coverage_metrics.csv

wgs_fine_hist.csv

wgs_hist.csv

wgs_overall_mean_cov.csv

wgs_contig_mean_cov.csv

N

Y

wgs_coverage_metrics.csv

wgs_fine_hist.csv

wgs_hist.csv

wgs_overall_mean_cov.csv

wgs_contig_mean_cov.csv

 

For each coverage region specified by the user:

qc-coverage-region-i_coverage_metrics.csv

qc-coverage-region-i_fine_hist.csv

qc-coverage-region-i_hist.csv

qc-coverage-region-i_overall_mean_cov.csv

qc-coverage-region-i_contig_mean_cov.csv

qc-coverage-region-i_full_res.bed if full_res report type is requested for qc-coverage-region-i

qc-coverage-region-i_cov_report.bed if cov_report report type is requested for qc-coverage-region-i

qc-coverage-region-i_callability.bed if GVCF mode is enabled and the callability or exome-callability report type is requested

Y

N

wgs_coverage_metrics.csv

wgs_fine_hist.csv

wgs_hist.csv

wgs_overall_mean_cov.csv

wgs_contig_mean_cov.csv

 

 

target_bed_coverage_metrics.csv

target_bed_fine_hist.csvtarget_bed_hist.csv

target_bed_overall_mean_cov.csv

target_bed_contig_mean_cov.csv

 

target_bed_callability.bed if GVCF mode is enabled

Y

Y

wgs_coverage_metrics.csv

wgs_fine_hist.csv

wgs_hist.csv

wgs_overall_mean_cov.csv

wgs_contig_mean_cov.csv

 

target_bed_coverage_metrics.csv

target_bed_fine_hist.csv

target_bed_hist.csv

target_bed_overall_mean_cov.csv

target_bed_contig_mean_cov.csv

target_bed_callability.bed if GVCF mode is enabled

 

For each coverage region specified by the user:

qc-coverage-region-i _coverage_metrics.csv

qc-coverage-region-i_fine_hist.csv

qc-coverage-region-i_hist.csv

qc-coverage-region-i_overall_mean_cov.csv

qc-coverage-region-i_contig_mean_cov.csv

 

qc-coverage-region-i_full_res.bed if full_res report type is requested for qc-coverage-region-i

qc-coverage-region-i_cov_report.bed if cov_report report type is requested for qc-coverage-region-i

qc-coverage-region-i_callability.bed if GVCF mode is enabled and the callability or exome-callability report type is requested

When --enable-metrics-compression is set to true, the 1 bp resolution coverage metrics output bed file (_full_res.bed) are compressed to bigwig format.