Question: Annotation of XHMM VCF file (CNV analysis)
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gravatar for nkausthu
17 months ago by
nkausthu20
nkausthu20 wrote:

Hi,

I have XHMM generated VCF file which contains the CNVs from exomes of 200 individuals. It would be really great if someone can suggest me how to annotate this VCF (I have annotated using annovar but I don't know whether this is best way to do CNV annotation). Is there any methodology available to incorporate the information from DGV (whether the called CNV is already known or not ).

cnv xhmm vcf annotation exome • 1.1k views
ADD COMMENTlink written 17 months ago by nkausthu20

Hi , which kind of annotation are you looking for ?

ADD REPLYlink written 17 months ago by Titus810

Basically I would like to know which all are the gene or genes involved in deletions or duplications. Along with that I need to know its a rare or a common cnv..

ADD REPLYlink written 17 months ago by nkausthu20

to check CNV common usually they use http://dgv.tcag.ca/dgv/app/downloads?ref=GRCh37/hg19 at lab but it's manual cheeking... For the annotation annovar is not bad maybe you can look at OMIM genes to classify by pathologies associated too.

ADD REPLYlink written 17 months ago by Titus810

Right now I am also checking manually by downloading the complete set of cnv from DGV. But wanted to figure out whether it could be automated. Looking at OMIM genes is one thing I thought of doing to identify cnvs for know disease causing genes. Again cnv of a new gene which is not yet associated with a particular condition is still difficult. For this purpose I want to use the information from control population as well as our in house frequency. But as such I am not finding any way to do this.

ADD REPLYlink written 17 months ago by nkausthu20

I understand your bio-informatic problematic, you can have look to bedtools (in particular http://bedtools.readthedocs.io/en/latest/content/tools/intersect.html) which is a good tool to compare genomic coordinates. To use it you will need to transform your data in a bed files. If you don't know a programming language you could use excel (even if it's not a recommended in bio-informatic in my point of view) to create your bed files and compare DVG and your XHMM results :)

Hope it's helping

ADD REPLYlink written 17 months ago by Titus810

Great!! Thank you so much for reminding about bedtools. I think this will work. Let me try. One more thing I want to know its regarding the allele count which is in Xhmm vcf file. Some times for a particular cnv vcf shows AC=3 and when I go back and check in .xcnv file only one individual has this cnv. Do you know what it means. I thought xhmm gives allele count equal to number of individuals.

ADD REPLYlink written 17 months ago by nkausthu20

Hi, strange think never saw that but could it be that XHMM found a CNV duplicates 2 times in your sample , it will mean that he got 3 times more coverage than the rest of you sample ?

ADD REPLYlink written 17 months ago by Titus810

Oks.. If this is the case I can't filter cnvs based on allele count. I generally consider AC=1,0 or 0,1 thinking that only one patient has the corresponding CNV. Then it's very difficult to analyse and narrow down to a pathogenic cnv

ADD REPLYlink written 17 months ago by nkausthu20

I don't know this is only an hypothesis did you check XHMM documentation to check the meaning of AC ?

ADD REPLYlink written 17 months ago by Titus810

From xhmm Google group, I could understand that ac corresponds to number of individuals.

ADD REPLYlink written 17 months ago by nkausthu20

Can you link me the information please ?

ADD REPLYlink written 17 months ago by Titus810

XHMM

ADD REPLYlink modified 17 months ago • written 17 months ago by nkausthu20

Yes, CNV annotation could be automated (OMIM, DGV, 1000g, haploinsufficiency, TAD, ... and also your own in-house information)!

You can look at this post describing the annotSV tool: Annotation for SV and CNV

ADD REPLYlink modified 9 months ago • written 9 months ago by LGMgeo90
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