Question: difference between Copy Number 0 and INDEL 1000genomes
0
gravatar for cocchi.e89
6 months ago by
cocchi.e8930
cocchi.e8930 wrote:

I am working with 1000 genomes VCF files that I need to annotate with some patients files, I noticed that some variants are annotated as structural variants, with indication <CN[number-of-CN]>. I was wondering if I can reconvert these variants to INDEL format, e.g.

*22-16050654 A <CN0> [...]*

could become:

*22-16050654 A . [...] ?*

Or:

*22-16050654 A <CN4> [...] ***-->*** 22-16050654 A AAAAA [...]*

Or it would bring to some conceptual error? Otherwise don't I risk to miss some INDELs? Thanks a lot in advance for any help!

sv cnv indel 1000g • 139 views
ADD COMMENTlink modified 6 months ago • written 6 months ago by cocchi.e8930

How were the structural variants called? - look up the respective program's documentation in order to find the correct interpretation of CN=0. Assuming it is deletion, I see no major issue in re-formatting it as an indel, but you have to state this in your methods.

ADD REPLYlink written 6 months ago by Kevin Blighe50k
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