Question: How to find the most commonly affected consensus copy number range given slightly different per sample range
0
gravatar for sebastianzeki0
4.8 years ago by
United Kingdom
sebastianzeki0170 wrote:

I have a load of files from different samples containing the chr  start end copyNumber

Each file represents one sample. There may be an overlap between samples in terms of copy number amplifications or deletions but the range doesn't always exactly match eg.

Sample 1

chr               start                end               copyNumber

1                   15000           15500                    2

1                   15500           16000                    2

 

Sample 2

chr               start                end               copyNumber

1                   15000           15500                    2

1                   15500           16000                    1

I want to find the common range where there is a deletion or amplification between samples (more then two up to 200) so in the above example it would be:

chr               start                end               copyNumber

1                   15000           15500                    2

 

Is there a tool to do this? Would bedtools do this- would a bed file be accepted if I put copy number data into it?

sequencing copy number • 1.8k views
ADD COMMENTlink modified 4.8 years ago by Biostar ♦♦ 20 • written 4.8 years ago by sebastianzeki0170
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2106 users visited in the last hour