Genome data available through IGV.js

Genomic data are available for browsing using IGV.js through the Interpretation Portal. A variety of data and files generated by the Rare Disease Pipeline are available to view, a summary of which is shown below. The most relevant files for review are shown in bold.

File	Description
[SampleID].repeats.vcf.gz	Short tandem repeat genotypes estimated by ExpansionHunter
[SampleID].enhanced.cnv.vcf.gz	Copy number variants detected by DRAGEN CNV in the proband. Including annotations for high quality small CNVs (2-10 kb) detected by DRAGEN CNV and DRAGEN SV
[SampleID].cnv.vcf.gz	Copy number variants detected by DRAGEN CNV in other family members
[SampleID].forceGT.vcf.gz	Genotypes of approximately 500,000 SNPs used for Genomic and Data Checks
[SampleID].FGT_SMS.SNP.vcf.gz	Genotypes of SNPs used by the Sample Matching Service
[referralID_XXXXX].duprem.left.split.vcf.gz	Small variants detected by the DRAGEN small variant caller after normalisation
[referralID_XXXXX].sv.vcf.gz	Structural Variants detected by DRAGEN SV, joint called for family members where available
[SampleID].GRCh38DecoyAltHLA_NonN_Regions_autosomes_sex_mt.CHR_full_res.bw	Genome coverage file
[SampleID].target.counts.bw	Intermediate file from DRAGEN CNV. This file can be used to review dropout regions for which CNV signals are not extracted from the alignments for inclusion in CNV calling. CNV events may span these intervals if there is sufficient signal in flanking regions.
[SampleID].cram	Genome alignment (CRAM format) generated by the DRAGEN aligner