Files

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

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BAM Files —Aligned sequences and quality scores in the BAM (*.bam) file format.

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VCF Files —Variant calls in the VCF (*.vcf.gz) file format.

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Genome VCF Files —Variants, references, and no calls for all sites in the genome VCF (gVCF) file format.

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Sample ID Files —Sample ID information for each sample.

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Summary File —Statistics for each sample.

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Genotypes of Interest Files —Genotypes of user provided positions in the VCF file format (*.genotype.vcf) and the CSV file format (*.genotype.csv).

The following is the complete list of output files:

File name	Description
<SampleName_S#>.annotations.json.gz	Variant annotation in JSON produced by the Illumina Annotation Engine. Produced only if variant annotation is performed.
<SampleName_S#>.bam	Alignments in BAM
<SampleName_S#>.bam.bai	BAM index file
<SampleName_S#>.baseCoverage.csv	CSV file containing aligned bases for each target.
<SampleName_S#>.coverage.csv	CSV file containing number of aligned reads for each target.
<SampleName_S#>.coverage.plot.csv	CSV file containing data for the coverage plot in the report.
<SampleName_S#>.geneAmpliconUniformity.csv	Gene-wise amplicon coverage uniformity CSV file. Produced only when the Gene ID column is populated in the Probes section of the manifest file.
<SampleName_S#>.genome.vcf.gz	Genome VCF file
<SampleName_S#>.genome.vcf.gz.tbi	Genome VCF tabix index file
<SampleName_S#>.genotype.csv	Genotypes of interest CSV file. Produced only when Genotypes of Interest VCF files are provided.
<SampleName_S#>.genotype.vcf	Genotypes of interest VCF file. Produced only when Genotypes of Interest VCF files are provided.
<SampleName_S#>.pisces.bam	Stitched and optionally indel-realigned alignments used for variant calling in BAM format.
<SampleName_S#>.pisces.bam.bai	BAM index file
<SampleName_S#>.report.html	HTML report
<SampleName_S#>.report.pdf	PDF report
<SampleName_S#>.sampleID.csv	Sample ID CSV file. Produced only if Sample Identification is performed.
<SampleName_S#>.sampleID.fingerprint.txt	Sample ID fingerprint file. Produced only if Sample Identification is performed.
<SampleName_S#>.sampleID.vcf	Sample ID VCF file. Produced only if Sample Identification is performed.
<SampleName_S#>.snvsContextCounts.csv	CSV file containing the number of variants by type and context
<SampleName_S#>.summary.csv	CSV file containing summary metrics
<SampleName_S#>.variantFrequencyCounts.csv	CSV file containing the binned variant frequency
<SampleName_S#>.varianttable.txt	Data file for the small variant table in the report. Produced only if variant annotation is performed.
<SampleName_S#>.vcf.gz	Variant-only VCF file
<SampleName_S#>.vcf.gz.tbi	Variant-only VCF tabix index file

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Files