Question: Identifying CNVs from targeted amplicon sequencing
0
gravatar for kvn95ss
10 months ago by
kvn95ss0
kvn95ss0 wrote:

I have few unmatched samples which have been sequenced with targeted amplicon sequencing using a custom library which covers a small segment of a chromosome (less than 300kb in length). The samples have been aligned to a BAM file and now I have to check for copy number variants.

I've used CNVkit to detect CN regions, however the docs mention that it's better if the sequenced regions span greater than million bases in length. I've also used ONCOCNV but it fails to detect any CN regions (although visually the shift in CN is visible).

Since only small region of the samples are covered, are there any other tools I can use, or do I have to filter the CN regions manually? Are there any papers which can help me out on how to manually filter out CN regions for the small segments?

ADD COMMENTlink modified 10 months ago by mkulecka300 • written 10 months ago by kvn95ss0
2

Maybe you could have a look at COV'COP : git, publication.

ADD REPLYlink written 10 months ago by erwan.scaon670

I know that some people at my institute are using HMMcopy. I am not sure of its performance on targeted NGS. There are so many NGS copy number tools such that it's difficult to know which ones are best. The earlier ones that were released typically did not adjust for GC content, which renders their utility as minimal.

ADD REPLYlink modified 10 months ago • written 10 months ago by Kevin Blighe41k
2
gravatar for geocarvalho
10 months ago by
geocarvalho110
Brazil/Recife
geocarvalho110 wrote:

I have been collecting some papers about CNV analysis (link). There is a topic about Amplicon sequencing (AS). Nowadays, I'm using Exomedepth+cnvScan. I tested CoNVaDING, but didn't have good results with my data. Now I'm testing VisCap.

Cheers.

ADD COMMENTlink written 10 months ago by geocarvalho110

Dear geocarvalho,

Do you still use Viscap ?

Thanks

ADD REPLYlink written 6 weeks ago by luckyluke950

I didn't finish my benchmark, but I helped a friend to use it!

ADD REPLYlink written 6 weeks ago by geocarvalho110

Valeu cara.

ADD REPLYlink written 6 weeks ago by Kevin Blighe41k
1

hahahah por nada! XD

ADD REPLYlink written 6 weeks ago by geocarvalho110
0
gravatar for mkulecka
10 months ago by
mkulecka300
European Union
mkulecka300 wrote:

I have used CONTRA (https://www.ncbi.nlm.nih.gov/pubmed/22474122). This software is supposedly tuned for targeted sequencing.

ADD COMMENTlink written 10 months ago by mkulecka300
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