difference between Copy Number 0 and INDEL 1000genomes
0
0
Entering edit mode
2.5 years ago
cocchi.e89 ▴ 170

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!

1000g indel sv cnv • 425 views
ADD COMMENT
0
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 2205 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6