Question: How to call CNV(copy number variant) in Pacbio ?
1
gravatar for qincai158
2.5 years ago by
qincai15810
qincai15810 wrote:

Hi, I have some data on rice.BWA software is used for sequence alignment, Be based for alignment result,I get many structural variants called by sniffles ,Now I want to get copy number variant. I don't know what to do.Can you recommend some software that can detect CNV(copy number variant ) ?

 I'll appreciate your help!
sequence alignment gene • 1.0k views
ADD COMMENTlink written 2.5 years ago by qincai15810

CPV is type of SV specially deletion or duplication which both identified by Sniffles . Their is exact thread for what you asked (specially that you used sniffles ):

How to group CNV

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by Medhat8.8k

Thank for your reply ! How to judge copy number variants from deletion or duplication or vcf file?

ADD REPLYlink written 2.5 years ago by qincai15810

You can count both as CNV

ADD REPLYlink written 2.5 years ago by Medhat8.8k

Thank for your reply! But Sniffles software get duplication which contains Tandem duplication and Dispersed duplication, CNV refers to Tandem duplication. How to abstract tandem duplication from duplication? Do you agree my idea ?

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by qincai15810

CNV refers to Tandem duplication

I don't think I agree here. An element which is duplicated will have a higher copy number, regardless whether the duplication is in tandem or dispersed.

ADD REPLYlink written 2.5 years ago by WouterDeCoster44k

Sniffles detects structural variants, which include copy number variants. So you already have copy number variants.

ADD REPLYlink written 2.5 years ago by WouterDeCoster44k

Thank for your reply ! I read an artical named "Detection and assessment of copy number variation using PacBio long-read and Illumina sequencing in New Zealand dairy cattle". The author grouped DUP and DEL called by Sniffles as CNV . Here is the original words in the artical:

Sniffles software identified a total of 38,709 putative SV, of which 19,797 were CNV (deletions, n = 18,577; duplications, n = 1,220) in a PacBio sequence generated from Esteem’s DNA. Of the 3,532 CNV (deletions, n = 3,055; duplications, n = 477) that remained after filtering, 899 (deletions, n = 740; duplications, n = 159) and 126 (deletions, n = 76; duplications, n = 50) overlapped by at least 1 bp with Ensembl (build 84; http:// mar2016.archive.ensembl.org/index.html) annotated genes and exons, respectively (Table 1).

I am not sure whether he is right.

ADD REPLYlink written 2.5 years ago by qincai15810

A copy number variant is an element of which the amount varies in the genome. You have for example more or less copies of gene x. A deletion or a duplication is a copy number variant: you have more or less of a feature.

ADD REPLYlink written 2.5 years ago by WouterDeCoster44k
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