Hello
for WGS, when a given depth of coverage is recomended, for example: 30x for variant calling, where does that quantitiy derive from?:
A/ from raw reads (number of reads * read length / genome size)
B/ from raw reads minus the duplicate percentage. ( (number of reads-%duplication) * read length / genome size)
C/ from raw alignments after filters are applied (i.e. map quality and base quality >= 20)
D/ from processed alignments (i.e. after base quality score recalibration) after filters are applied (i.e. map quality and base quality >= 20)
I have been searching through several threads in this forum and in the literature, but I find no consensus on depth of coverage calculation. I am mostly confused about wheather it takes into account the reads before or after alignment.
Is there any?
Thanks in advance
In which case then
read depth
would be equivalent to option A andcoverage
would be equivalent to option D.would you agree?