VCF merge containing CNV

Question

[Andrea Spinelli]

Hello everybody, like the title: which is the way to merge VCFs files containing CNV?

I use vcf-merge (https://vcftools.github.io/perl_module.html#vcf-merge), a VCFtools function, and after bgzip and tabix (http://www.htslib.org/doc/tabix.html), SAMtools, to indexing and tab separating variants, but I don't know if it is the right way. Thanks.

[Kevin Blighe]

Why would a VCF contain CNV? / Perché un VCF contenesse CNV? /

A copy number variant is generally defined as a region > 1 kilobase. VCF files should only contain single nucleotide variants and short insertions/deletions (InDels). If you have a customised VCF format, then the standard tools used to manipulate VCF files may not understand how to interpret your custom format. In that case, you could use Python scripts to manipulate your VCF files. I have done this recently to include copy number variants in my custom VCF format.

Kevin

[DG]

Structural variants, including CNVs, have been allowed in VCFs according to the specification for quite some time. You can get into adding custom tags for ease of use (like SVEND is often used to give easy reference to stop coordinates). While it may well be that a caller may be adding custom fields to the INFO line it is incorrect to say that only short Indels and SNVs should be in a VCF file.

Answer 1

[DG]

Whether vcf-merge works for what you are doing or not I'm not actually sure off hand. However, since you have a solution you have tried the answer is to test that solution. Take some sample VCFs with the type of variants you want to merge, run vcf-merge, and look at the results. Do you get what you would expect?

If vcf-merge doesn't do what you expect you may want to try the ensemble method from bcbio.variation.recall