difference between Copy Number 0 and INDEL 1000genomes
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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
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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.