Minimum (ir maximum) bam depth/coverage for structural variation analyses

linudz · 07-05-2017, 06:44 AM

*or maximum

We are studying structural variation in several plant genomes Illmumina pair-end DNA re-sequencing, and noticed that the number of deletions in some samples (PINDEL) drops significantly. After having boldly calculated the depth as

[number of reads] x mean read length / genome size

we noticed that in these samples the depth was way lower (around 10 folds on an average of 50).

I was wondering if there is some lower or higher limit in a sample depth to start considering an adulterated result.

Thanks.

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07-05-2017, 06:44 AM	#1
linudz Junior Member Location: Rome Join Date: Feb 2017 Posts: 3	Minimum (ir maximum) bam depth/coverage for structural variation analyses *or maximum We are studying structural variation in several plant genomes Illmumina pair-end DNA re-sequencing, and noticed that the number of deletions in some samples (PINDEL) drops significantly. After having boldly calculated the depth as [number of reads] x mean read length / genome size we noticed that in these samples the depth was way lower (around 10 folds on an average of 50). I was wondering if there is some lower or higher limit in a sample depth to start considering an adulterated result. Thanks.