How do you know the best segments in cnvkit after filtering?
1
0
Entering edit mode
4.6 years ago
Jordan ★ 1.3k

Hi,

I'm working on WGS data using cnvkit. I filtered the segments using segmetrics and call. Here are my steps:

cnvkit.py segmetrics tumor.cnr -s tumor.cns --ci --sem -o tumor.segmetrics.cns
cnvkitpy call tumor.segmetrics.cns --filter ci -o tumor.segmetrics.call.cns

I have about 300 segments at the end of this step. Is there a way to tell, which are statistically the best segments?

For e.g., two rows in tumor.segmetrics.call.cns file looks like this.

chromosome      start   end     gene    log2    cn      depth   probes  weight
chr1    125086529   125146265   -   0.0648392   2   143.179 52  44.4282
chr1    125146265   125175570   -   -1.35037    0   71.7419 24  14.5482

Is there a way to tell which segment you trust more? I understand that, more the weight better the reliability.

But I was wondering how you would normally pick the best segments?

Thanks in advance!

cnvkit wgs cnv • 1.9k views
ADD COMMENT
1
Entering edit mode
4.6 years ago
brunobsouzaa ▴ 830

What helps me on my analysis is: - get only cn values that are not 2; - output the ref depth for each segment on the spreadsheet and the depth ratio. - correlate the cn values with depth ratio and weight!

Also you can build your own database with the most frequent calls on different samples!

Hope it helps.

ADD COMMENT
1
Entering edit mode

Thank you! Looking at the weight and CN values looks like the best way to go.

ADD REPLY
0
Entering edit mode

Try adding another CNV caller to your analysis and choose common results!

ADD REPLY

Login before adding your answer.

Traffic: 1507 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