We are developing a pipeline to identify plant SNPs and Structural variations. As a part of checking, we have to separate a plant genome in different X coverage. For instance, actual genome data coverage is 40 X, now we need to generate it in different X coverage like 10X, 20x and 30x. Is it possible? If yes please help me.
If you're downsampling the WGS experiment across entire genome, simple
samtools view -s would do it. Just be careful with using different seeds each time if you're doing repetitive subsampling, otherwise each time would generate the exact same subsample.