Hi,
I have created contaminated human sequence R1, R2 fq.gz files by adding 10% random sequences from another human sample. When I align to the reference genome, the average coverage is around 1.0x.
I have tried to detect the contamination with verifybamid and also GATK GetPileupSummaries/CalcualteContamination but the the contamination is not detected.
Has anyone been successful detecting contamination on low coverage .bam files with coverage around 1.0x?
Thanks.