copy number profiling from shallow sequenzing or whole genome low coverage seq for mouse genome

Question

[ifudontmind_plzz]

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.

[Sean Davis]

Are these tumor/normal samples, or simply from a population?

[ifudontmind_plzz]

@Sean , i have only mouse tumor samples

Answer 1

[Eric T.]

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.

Answer 2

[bruce.moran]

You can use the QDNAseq package in Bioconductor, pretty straight forward to get running if you can use R.

Answer 3

[ifudontmind_plzz]

@bruce, i doubt QDNAseq is tailored for only human genome not for mouse

[bruce.moran]

Sorry, you are correct. You could make your own annotation but that will not be as straight forward...