Impacts of low coverage depths and post-mortem DNA damage on variant calling: a simulation study

Area of Science:

• Genomics
• Bioinformatics
• Paleogenetics

Background:

• Massively parallel sequencing is suitable for ancient DNA (aDNA) studies.
• Short-read alignment for variant identification faces challenges from low DNA concentrations and post-mortem DNA damage.

Purpose of the Study:

• To investigate the impact of DNA damage and sequencing depth on variant identification from short-read alignment in silico.
• To assess the accuracy and recovery of variants under simulated ancient DNA conditions.

Main Methods:

• Simulated reference and sample genomes with varied GC content and divergence.
• Generated short-read pools with simulated post-mortem DNA damage (fragmentation, biases, transition rates).
• Analyzed alignment success and variant recovery across different read lengths, divergence levels, and sequencing depths.

Main Results:

• Alignment success decreased with increased read length and increased with divergence.
• Variant recovery decreased with increased divergence.
• SNP identification accuracy was lower for high damage/low divergence samples.
• Increased sequencing depth significantly improved total variant recovery.

Conclusions:

• In silico ancient DNA damage patterns minimally affect variant call accuracy and recovery.
• Modest increases in sequencing depth substantially enhance variant recovery in aDNA studies.