What should be the minimum read depth of a minor allele for a reliable variant call? I would be needing some journal reference in that respect. I would like to cite it as a support for the choice made.
I think it depends strongly on the platform used of sequencing and (even more strongly) on your template. Are you sequencing genomic DNA or cDNA? Animal, plant or bacteria?
its DNA and its illumina paired end read. But if it was cDNA and illumina paired end reads, then what should be the cut off.
Wouldn't the paper below contained the answer to your question?
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3566181/
If you have genomic data from plant you can try this book:
http://library.wur.nl/WebQuery/wda/2002719
There is also another paper on the issue:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3706896/
This describes some issues related to different pipelines so it may be interesting to you.
@Marchin Thank you very much. But all these speaks for genomic DNA. It would serve my present requirement. Still I want to know the status for cDNA.
This is very interesting paper about trimming mRNA sequence data. Maybe this is what you looking for. ;-)
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3908319/
@Stephen
: the suggested paper is quite informative but not exactly the one I am looking for. Its about, read count cutoff for reliable variant call at a particular locus.
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