Question: Identifying CNVs from targeted amplicon sequencing
1
gravatar for kvn95ss
21 months ago by
kvn95ss10
kvn95ss10 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 7 months ago by lffu_003240 • written 21 months ago by kvn95ss10
2

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

ADD REPLYlink written 21 months ago by erwan.scaon750

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 20 months ago • written 20 months ago by Kevin Blighe54k
2
gravatar for geocarvalho
20 months ago by
geocarvalho130
Brazil/Recife
geocarvalho130 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 20 months ago by geocarvalho130

Dear geocarvalho,

Do you still use Viscap ?

Thanks

ADD REPLYlink written 11 months ago by luckyluke950

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

ADD REPLYlink written 11 months ago by geocarvalho130

Valeu cara.

ADD REPLYlink written 11 months ago by Kevin Blighe54k
1

hahahah por nada! XD

ADD REPLYlink written 11 months ago by geocarvalho130
0
gravatar for mkulecka
20 months ago by
mkulecka310
European Union
mkulecka310 wrote:

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

ADD COMMENTlink written 20 months ago by mkulecka310
0
gravatar for lffu_0032
7 months ago by
lffu_003240
lffu_003240 wrote:

you can try CONVector, it is designed for germinal CNV detection in the PCR-enriched targeted sequencing data. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5075217/pdf/12859_2016_Article_1272.pdf

ADD COMMENTlink written 7 months ago by lffu_003240

Please create a new Tool type post and showcase your tool. Bumping old posts with the same content comes across as spamming and is not encouraged.

ADD REPLYlink written 7 months ago by RamRS25k
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