Finding a known duplication mutation in a VCF file

Question

[langzvi]

Hello.
I have a VCF file in which I wish to look for a known disease-associated gene duplication mutation. Is there a command line program for that? I got VCFtools among others, but I couldn't find a proper command.

[Pierre Lindenbaum]

is it a small duplication or a SV/SNV ? better than a vcf would be to call the vCNV/SV from a bam with manta/smoove/delly etc....

[langzvi]

It's a gene with length of 35,548 nt according to NCBI, so it's pretty big. So, you suggest converting the VCF to a BAM file? The VCF is the only input file I got.

[Pierre Lindenbaum]

The VCF is the only input file I got.

so the only tool I know is bcftools roh but IMHO, you cannot check if there is a true positive without looking at a bam file;