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Old 08-13-2012, 06:10 AM   #1
yuhao
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Default effect to variation detection if the reads are not distributed uniformly

What happen if the sequenced reads don't distribute uniformly across the genome? What is the resulting effect for variation detection? Is there any qualitative research on this?I see many papers writing that "assume the reads are sampled randomly from the sample genome", but if it is not equally distributed, what will the result be?
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Old 08-13-2012, 03:41 PM   #2
DFJ111
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Hi, I am dealing with similar problems.. I am reading through this special edition, which might be useful..

http://genomebiology.com/content/12/9

I know that some assemblers (e.g. MIRA3 with uniform_read_distribution switch) have settings to not assume that read distribution is uniform. These seem to be mainly used for EST sequencing assembly but would also be relevant for exome sequencing. What effect that has, I don't know. I would assume that low coverage regions would be problematic: this paper (http://www.ncbi.nlm.nih.gov/pubmed/20980557) suggests that low coverage regions caused by heterogeneous coverage result in a high rate of false positive SNPs. Any experts want to help?
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