DRAGEN Germline with CNV Variant Calling

Primary Annotation Files

• bam​

• cnv.vcf.gz​

• control.CX_report.txt.gz​

• CX_report.txt.gz​

• gvcf.gz​

• vcf.gz​

• cnv_sv.vcf.gz (Note: This file will only appear if *cnv.metrics.csv has called CNVs and they're passing)

Primary Metrics Files

• cnv_metrics.csv​

• fastqc_metrics.csv​

• gvcf_metrics.csv​

• fragment_length_hist.csv​

• lambda_unmethylated_control.control.M-bias.txt​

• puc19_methylated_control.control.M-bias.txt​

• M-bias.txt​

• mapping_metrics.csv​

• methyl_metrics.csv​

• vc_metrics.csv​

• wgs_contig_mean_cov.csv​

• wgs_coverage_metrics.csv​

• wgs_overall_mean_cov.csv

Mapping / Alignment Metrics

The following can be extracted from *mapping_metrics.csv files:

• Total reads​

• Total bases​

• Mapped reads percentage​

• Paired reads mapped to different chromosomes (MAPQ>=10) percentage​

• Mismatched bases R1 (excl. indels) percentage​

• Mismatched bases R1 (excl. indels) percentage​

• Q30 bases percentage​

• Not properly paired reads (discordant) percentage​

• Percentage of duplicate marked reads​

• Percentage of reads with MAPQ > 40​

• Soft-clipped bases R1​

• Soft-clipped bases R2

Coverage Metrics

The following can be extracted from *wgs_coverage_metrics.csv files:

• Uniformity of coverage, percent of bases with coverage > 0.2 * mean coverage​

• PCT of genome with coverage [0x: 1x)​

• Average autosomal coverage over genome

Methylation Calling Metrics

The following can be extracted from *methyl_metrics.csv files:

• % of Cs methylated in CpG context (tag in csv file: mCpGPer)​

• % of Cs methylated in CHG context (tag in csv file: mCHGPer)​

• % of Cs methylated in CHH context (tag in csv file: mCHHPer)​

• % of Cs methylated in unknown context (tag in csv file: mCunkPer)​

• The same 4 %C methylation metrics will be reported for the lambda and puc19 control genomes

M-bias Metrics

The following can be extracted from *M-bias.txt files:

• Counts of methylated and unmethylated Cs

• % methylation and coverage for each position in read1 and read2 for CpG, CHG, and CHH contexts