Files
The Files page provides access to the output files for each sample analysis.
• | BAM Files—Aligned sequences and quality scores in the BAM (*.bam) file format. |
• | VCF Files—Variant calls in the VCF (*.vcf.gz) file format. |
• | Genome VCF Files—Variants, references, and no calls for all sites in the genome VCF (gVCF) file format. |
• | Summary File—Statistics for each sample. |
• | Picard HSmetrics Output |
• | Summary Statistics |
• | Report PDF |
• | Variant Table File |
• | BAM Files |
• | VCF Files |
• | Genome VCF Files |
• | Summary File |
• | Picard HSmetrics Output |
• | Summary Statistics |
• | Report PDF |
• | Variant Table File |
The following is the complete list of output files:
File name |
<SampleName>.time_metrics.csv |
<SampleName>.wgs_contig_mean_cov.csv |
<SampleName>.wgs_hist.csv |
/Additional Files/<SampleName>.wgs_overall_mean_cov.csv |
<SampleName>.wgs_ploidy.csv |
appVersion.log |
stdout.log |
<SampleName>.wgs_fine_hist.csv |
<SampleName>.wgs_coverage_metrics.csv |
<SampleName>.target_bed_callability.bed |
<SampleName>.target_bed_contig_mean_cov.csv |
<SampleName>.target_bed_coverage_metrics.csv |
<SampleName>.target_bed_fine_hist.csv |
<SampleName>.target_bed_overall_mean_cov.csv |
/Additional Files/<SampleName>.target_bed_hist.csv |
/Additional Files/<SampleName>.target_bed_ploidy.csv |
<SampleName>.qc-coverage-region-1_contig_mean_cov.csv |
<SampleName>.qc-coverage-region-1_coverage_metrics.csv |
<SampleName>.qc-coverage-region-1_fine_hist.csv |
<SampleName>.qc-coverage-region-1_hist.csv |
<SampleName>.qc-coverage-region-1_overall_mean_cov.csv |
<SampleName>.qc-coverage-region-1_ploidy.csv |
<SampleName>.qc-coverage-region-2_contig_mean_cov.csv |
<SampleName>.qc-coverage-region-2_coverage_metrics.csv |
<SampleName>.qc-coverage-region-2_fine_hist.csv |
<SampleName>.qc-coverage-region-2_hist.csv |
<SampleName>.qc-coverage-region-2_overall_mean_cov.csv |
<SampleName>.roh.bed |
<SampleName>.roh_metrics.csv |
(if annotation is enabled) /Additional Files/<SampleName>.annotations.json |
/Additional Files/<SampleName>.coverageHistogram.txt |
/Additional Files/<SampleName>.fragmentlength.csv |
/Additional Files/<SampleName>.report.pdf |
(if Picard is enabled) /Additional Files/<SampleName>.HsMetrics.txt |
(if Picard is enabled) /Additional Files/<SampleName>.PerTargetMetrics.txt |
/Additional Files/<SampleName>.summary.csv |
/Additional Files/<SampleName>.varianttable.txt |
If output format is set to BAM, the following Map/Align files are generated |
<SampleName>.mapping_metrics.csv |
<SampleName>.bam |
<SampleName>.bam.bai |
<SampleName>.bam.md5sum |
If somatic variant calling is enabled, the following files are generated |
<SampleName>.baf.bw |
<SampleName>.hard-filtered.baf.bw |
<SampleName>.hard-filtered.vcf.gz |
<SampleName>.hard-filtered.vcf.gz.md5sum |
<SampleName>.hard-filtered.vcf.gz.tbi |
<SampleName>.vc_metrics.csv |
<SampleName>.vcf.gz |
<SampleName>.vcf.gz.md5sum |
<SampleName>.vcf.gz.tbi |
If germline variant calling is enabled, the following files are generated |
<SampleName>.baf.bw |
<SampleName>.hard-filtered.baf.bw |
<SampleName>.hard-filtered.gvcf.gz |
<SampleName>.hard-filtered.gvcf.gz.mdsum |
<SampleName>.hard-filtered.gvcf.gz.tbi |
<SampleName>.vc_metrics.csv |
<SampleName>.hard-filtered.vcf.gz |
<SampleName>.hard-filtered.vcf.gz.tbi |
If CNV is enabled, the following files are generated |
<SampleName>.combined.counts.txt |
<SampleName>.cnv.gff3 |
<SampleName>.cnv.vcf.gz |
<SampleName>.cnv.vcf.gz.md5sum |
<SampleName>.cnv.vcf.gz.tbi |
<SampleName>.cnv_metrics.csv |
<SampleName>.target.counts |
<SampleName>.target.counts.bw |
<SampleName>.target.counts.gc-corrected |
<SampleName>.seg |
<SampleName>.seg.bw |
<SampleName>.seg.called |
<SampleName>.seg.called.merged |
<SampleName>.tn.bw |
<SampleName>.tn.tsv |
<SampleName>.improper.pairs.bw |
If SV (Manta) is enabled, the following files are generated |
<SampleName>.sv.vcf.gz |
<SampleName>.sv.vcf.gz.tbi |
<SampleName>.sv_metrics.csv |