How to Import a Marker File for Sample Identity Monitoring?

What are Identity Markers?

Identity markers are single nucleotide polymorphisms (SNPs) used for:

• Sample identity verification (sample tracking)
• Detecting sample swaps or contamination
• Quality control across runs

Markers typically use common SNPs with:

• High heterozygosity rates
• Well-defined genotypes
• No clinical significance (non-pathogenic)

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Compatible worksets

Markers are analyzed in the ID Check tab of analyses for the following worksets (when configured):

• GermlineVar and GermlineFamily (version ≥ 2.3)
• GermVar (version ≥ 3.1)
• SomaVar (version ≥ 2.5)
• SomaVar LF (version ≥ 2.1)
• SomaCGP (version ≥ 0.6)

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How to Import Markers?

Step 1: Access the Marker Tab

1. Go to Entity Settings → Markers
2. Click on "+ Add marker"

Step 2: Prepare Your Marker File

File requirements:

• Format: .tsv or .txt (tab-separated)
• Must include header row
• Five required columns:

Column definitions:

• CHR: Chromosome (format: chr1, chr2, chrX, chrY)
• ID: Marker identifier, typically rsID from dbSNP
• POS: Genomic position (must match your genome reference)
• REF: Reference allele (A, C, G, or T)
• ALT: Alternative allele (A, C, G, or T)

Example .tsv file:

CHR	ID	POS	REF	ALT chr1	rs1234567	1000000	A	G chr1	rs2345678	1500000	C	T chr2	rs3456789	2000000	G	A 

Step 3: File Limitations

⚠️ Maximum 100 lines including the header

This means you can include up to 99 markers in a single file.

Step 4: Upload the File

1. From the Markers tab, after you click + Add marker, select the genome reference (GRCh37 or GRCh38).
   
2. Click "+ Add a file" 
3. Select you marker file from your computer
4. Click "Create"

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Automatic ID Check

Once markers are configured, the platform will automatically:

1. Genotype the markers for each sample during analysis, measuring genotype match, VAF, alternate read count (AO), and coverage at each marker position.
2. Display results in two places, at different scopes:
   • Analysis level — the "ID check" tab in that analysis's QC section, with one row per marker and columns for GT (match indicator), VAF, AO, and coverage.

1. • Project level — the "ID check summary" in the project's QC tab, with one row per sample and one column per marker, showing a filled or empty circle to indicate a match at a glance across every sample in the project — useful for spotting swaps between different analyses or runs.

Viewing ID Check Results

• Analysis view: rows = markers, columns = GT / VAF / AO / COV for that sample.

• Project view: rows = samples, columns = markers, cells = filled (●) or empty (○) indicator.