Best practice to identify Copy number alteration from mouse whole genome low coverage sequencing study

Question

[ifudontmind_plzz]

Hi,

What could be the better tool to identify copy number alteration of mouse whole genome low coverage sequencing study (BAM file)?

[PoGibas]

What do you mean by "best way"? Is it what tool to use? If so, there were many such questions here on biostars: Recommendation For Cnv Calling Program Based On Depth Of Coverage From Bam

[ifudontmind_plzz]

@Pgibas, Yes I mean tools. Thank you

[Ashutosh Pandey]

Is it a inbred strain? If yes, you can try https://www.sanger.ac.uk/resources/software/cnd . It has been specifically designed for the inbred strains but I am not sure how it will perform for a low coverage study.

[ifudontmind_plzz]

it is not purely a inbred strain.

Answer 1

[h.mon]

This paper claims to have the most accurate method to detect CNV from low-coverage sequencing. I am halfway through it and did not find link to sources / executables. And of course, always take with a grain of salt non-independent software comparisons. Their introduction cites a bunch of other software as well.