genome coverage

[marco12345]

Hi,

Which one do you think is the best and easier alternative to Picard Statistics to measure basic genomic metrics, such as virus genome coverage?

I am working on Mac OSX's Terminal and Linux.

Thanks!

[Dario1984]

If you like working in R, then you can use the package Rsamtools to read in the mapping file and GenomicRanges to get coverage for every base, then divide by the size of the genome to calculate how many times you covered the genome.