Coverage/Callability Reports Over Custom Regions

DRAGEN generates the following coverage reports:

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A set of default reports for either the whole genome, or, if the --vc-target-bed option is specified, for the target region.

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Optionally, additional reports for up to three regions of interest (coverage regions).

To generate coverage region reports, use the –qc-coverage-region-i option, where i is 1, 2, or 3.

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Each –qc-coverage-region-i option requires a bed file argument.

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Regions in each bed file can be optionally padded using the --qc-coverage-region-padding-i option, which defaults to 0.

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A set of default reports is generated for each region.

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Optionally, additional reports can be specified for each region by using the –qc-coverage-reports-i option.

The following example shows the options required to generate coverage reports.

$ dragen … \
--qc-coverage-region-1 <bed file 1> \
--qc-coverage-reports-1 full_res \
--qc-coverage-region-2 <bed file 2> \
--qc-coverage-region-3 <bed file 3> \
--qc-coverage-reports-3 full_res cov_report

Counting Reads and Bases

All default and optional coverage reports listed in and use the following default rules for counting reads and bases:

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Duplicate reads are ignored.

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Soft and/or hard-clipped bases are ignored.

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Reads with MAPQ=0 are ignored.

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Overlapping mates are double-counted.

Nondefault settings:

The reports are available with or without running either the mapper and aligner, or the variant caller. However, the --enable-sort options must be set to true (the default is true).

By default overlapping mates are double counted. Set --qc-coverage-ignore-overlaps=true to resolve all of the alignments for each fragment and avoid double-counting any overlapping bases. This might result in marginally longer run times. This option also requires setting --enable-map-align=true. --gc-coverage-ignore-overlaps is a global setting and updates all qc-coverage-reports.

By default soft-clipped bases are not counted towards coverage. Set --qc-coverage-count-soft-clipped-bases=true to include soft-clipped bases in the coverage calculations. --qc-coverage-count-soft-clipped-bases is a global setting and updates all qc-coverage reports.

Any combination of the optional reports can be requested for each region. If multiple report types are selected per region, they should be space-separated.

It is possible to override the min MAPQ and min BQ to apply for a given region using the qc-coverage-filters.

A coverage filter is enabled by using one of the --qc-coverage-filters-i options (where i is 1, 2, or 3), in combination with the associated --qc-coverage-region-i option:

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--qc-coverage-region-i=<targetedregions.bed>

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--qc-coverage-filters-i <filters string>

For example, the following options are used to enable 1 bp resolution coverage output with filtering:

--qc-coverage-region-1 <targetedregions.bed>

--qc-coverage-filters-1 'mapq<10,bq<30'

--qc-coverage-reports-1 full_res

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The argument syntax is mapq<value,bq<value, which means that reads that have a mapping quality less than the specified value are not counted, and/or bases with a base call quality below the specified value.

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Valid filter arguments are mapq and bq only. Either, or both, can be specified.

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Only one operator < is supported. <=, >, >=, = are not supported.

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When filtering is enabled for a targeted region, DRAGEN outputs the filtered report files for this region. Unfiltered report files are not output for the targeted filtered region.

Callability for the Custom Regions

If the --qc-coverage-region-i option is used with --qc-coverage-reports-i (where i is 1, 2, or 3), callability can be added as a report type for that region. The output is a qc-coverage-region-i_callability.bed file. For each specified qc-coverage-region-i file, the average callability is reported in the variant calling metrics file. The padding size specified by the --qc-coverage-region-padding-i is used and overlapping regions are merged.

The optional min MAPQ and min BQ filters only influence read and base counting and do not influence the callability reports.

Contig lengths and region of interest lengths (used as denominators) do not include regions with N in the FASTA.

Available Report Types

Default Report

File Name	Description
_coverage_metrics.csv	Coverage Metrics Report
_fine_hist.csv	Fine Histogram Coverage Report
_hist.csv	Histogram Coverage Report
_overall_mean_cov.csv	Overall Mean Coverage Report
_contig_mean_cov.csv	Per Contig Mean Coverage Report
_ploidy.csv	Predicted Ploidy Report

Optional Reports

File Name	Description
_full_res.bed	Full Res Report
_cov_report.bed	Coverage Report
_callability.bed	Callability Report