Best practice to identify Copy number alteration from mouse whole genome low coverage sequencing study
Hi,
What could be the better tool to identify copy number alteration of mouse whole genome low coverage sequencing study (BAM file)?
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Ram
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ifudontmind_plzz
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ifudontmind_plzz
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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.
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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
@Pgibas, Yes I mean tools. Thank you
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.
it is not purely a inbred strain.