domains / families / science / duplicate-handling

duplicate-handling

separate

Mark and remove PCR/optical duplicates using samtools fixmate and markdup. Use when preparing alignments for variant calling or when duplicate reads would bias analysis.

When to use

• Mark or remove duplicate reads
• Prevent duplicate bias in variant calling
• Germline WGS / WES duplicate handling
• Somatic tumor/normal duplicate handling
• Exome / target capture duplicate handling
• ATAC-seq duplicate handling
• Ancient DNA duplicate handling
• PacBio HiFi amplicon duplicate handling

When not to use

• Bulk RNA-seq (no UMIs)
• Bulk RNA-seq (with UMIs)
• scRNA (10x, STARsolo, drop-seq)
• ctDNA / liquid biopsy / deep panel (UMI)
• Twist / IDT / Roche UMI capture
• Amplicon / hotspot panel (no UMI)
• Amplicon / hotspot panel (UMI)
• Long-read native (ONT, PacBio HiFi unamplified)

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