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