Best practice to identify Copy number alteration from mouse whole genome low coverage sequencing study
1
2
Entering edit mode
9.8 years ago

Hi,

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

next-gen-sequencing • 2.8k views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

@Pgibas, Yes I mean tools. Thank you

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

it is not purely a inbred strain.

ADD REPLY
0
Entering edit mode
9.5 years ago
h.mon 35k

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.

ADD COMMENT

Login before adding your answer.

Traffic: 1737 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6