Detect CNVs from SNP data

Question

[misbahabas]

Hello

Please tell me, is it possible to detect CNVs from SNP data?

Thanks to all

Answer 1

[guillaume.rbt]

Hi,

By SNP data do you mean that you have a vcf file? From this kind of data it's difficult to call CNVs.

However, if you have the alignments from which the SNPs have been called (bam files) you can run CNV detection tools as pindel, CNVnator or breakdancer ( https://omictools.com/cnv-detection3-category ).

Answer 2

[misbahabas]

thanks for reply

yes,

I have VCF files contains only SNP data of non human genome , Now I want to detect CNVs from that data