I am curious to know if there any available tools for analysing the copy number variation of mouse data generated from shallow-seq or whole genome low coverage seg.
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ifudontmind_plzz
You could use CNVkit on your dataset. I recommend making a BED file of the full-length genes of interest in the genome -- preferably non-overlapping, probably using bedtools; no need to be comprehensive, but you can if you like. Then run CNVkit with equal "target" and "antitarget" bin sizes, aiming for about 200-300 reads per bin, e.g. 10000 bp for 0.5-fold coverage.
You can use the QDNAseq package in Bioconductor, pretty straight forward to get running if you can use R.
@bruce, i doubt QDNAseq is tailored for only human genome not for mouse
Sorry, you are correct. You could make your own annotation but that will not be as straight forward...
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Are these tumor/normal samples, or simply from a population?
@Sean , i have only mouse tumor samples