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Files

The Files page provides access to the output files for each sample analysis.

• Alignment Files—Aligned sequences and quality scores in the BAM (*.bam) or CRAM (*.cram) 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. These files are generated only when the small variant caller output is set to gVCF.
• Summary File—Statistics for each sample.
• Genotypes of Interest Files—Genotypes of user provided positions in the VCF file format (*.genotype.vcf) and the CSV file format (*.genotype.csv).
• BAM or CRAM Files
• VCF Files
• Genome VCF Files
• Summary File
• Genotypes of Interest Files

The following is the complete list of output files:

File name

<SampleName>-replay.json

<SampleName>.time_metrics.csv

<SampleName>.wgs_contig_mean_cov.csv

<SampleName>.wgs_hist.csv

<SampleName>.wgs_overall_mean_cov.csv

<SampleName>.wgs_ploidy.csv

appVersion.log

stdout.log

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 output format is set to CRAM, the following Map/Align files are generated

<SampleName>.mapping_metrics.csv

<SampleName>.cram

<SampleName>.crai

If small variant calling is enabled, the following files are generated

<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 CNV is enabled, the following files are generated

CNV VCF (including TBI and md5sum)

Segmentation files

• <sample>.seg
• <sample>.seg.bw
• <sample>.seg.called
• <sample>.seg.called.merged

Target count files

• <sample>.target.counts
• <sample>.target.counts.bw
• <sample>.target.counts.gc-corrected

Diploid files

• <sample>.target.counts.diploid.bw

<SampleName>.tn.bw

<SampleName>.tn.tsv

<SampleName>.improper.pairs.bw

If Expansion Hunter is enabled, the following files are generated

<SampleName>.repeats.bam

<SampleName>.repeats.vcf.gz

<SampleName>.repeats.vcf.gz.tbi

If SV (Manta) is enabled, the following files are generated

<SampleName>.sv.vcf.gz

<SampleName>.sv.vcf.gz.tbi

<SampleName>.sv_metrics.csv