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. |
| • | Sample ID Files—Sample ID information for each sample. |
| • | 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 Files |
| • | VCF Files |
| • | Genome VCF Files |
| • | Sample ID Files |
| • | Summary File |
| • | Genotypes of Interest Files |
The following is the complete list of output files:
|
File name |
|
<SampleName>-replay.json |
|
<SampleName>.insert-stats.tab |
|
<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 (for CRAM, this will be a .cram) |
|
<SampleName>.bam.bai (for CRAM, this will be a .crai) |
|
<SampleName>.bam.md5sum (for CRAM, this will not exist). |
|
<SampleName>.pcr-model-0.log |
|
<SampleName>.pcr-model.log |
|
If output format is set to CRAM, the following Map/Align files are generated |
|
<SampleName>.mapping_metrics.csv |
|
<SampleName>.cram |
|
<SampleName>.crai |
|
<SampleName>.pcr-model-0.log |
|
<SampleName>.pcr-model.log |
|
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 |
|
<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 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 |