Hi,
I can't find an answer to my questions about one of the DepthOfCoverage output files, so I am asking you guys directly.
Here're the top lines of one of my interval_summary files
Target total_coverage average_coverage 011A_total_cvg 011A_mean_cvg 011A_granular_Q1 011A_granular_median 011A_granular_Q3 011A_%above_1 011A%above_10 011A%_above_20
C31761850:1971-2195 13420 59.64 13420 59.64 56 64 69 100.0 100.0 100.0
C31761850:2296-2432 4615 33.69 4615 33.69 30 37 40 100.0 100.0 97.8
C31762344:3316-3437 5061 41.48 5061 41.48 37 45 47 100.0 100.0 100.0
C31762344:3496-3578 2027 24.42 2027 24.42 23 26 27 100.0 100.0 100.0
Questions: how does DepthOfCoverage actually calculate "total_coverage" and "average_coverage"? What are the information it actually uses (coverage per base, per interval, or whatever else)?
I guess the coverage numbers are the same between columns 2/4 and 3/5 because I have only one sample here, correct?
Any help with this will be so much appreciated.
Best,
Claudio