alternative to vcftools for vcf v4.1

[Rcucullatus]

Hi everyone,

I need to retrieve some basic information from a vcf file of whole genome reads mapped to a reference, such as coverage, nucleotide diversity, etc.. I found vcftools to do all I needed, but my vcf files are in version 4.1 which is not supported by the vcftools binary executable, and I can't seem to find a linux alternative for this. Anyone has any suggestions?

Thanks!

[sam123sam]

The latest versions of VCFtools do support v4.1 - what version are you using? I suggest you update.

[Rcucullatus]

Hi, thanks for your help. I'm using version 0.1.9. To be fair though, the problem is that I tried to retrieve average depth from my vcf file with the "vcftools input.vcf --depth" command and although everything looked fine with the analysis, the output had "nan" in the column when I expected the average coverage do be. I the assumed this might be due to the lack of support for vcf v4.1 (as I understand it is only supported in the perl scripts and not in the binary executable), but I might be wrong of course.

[sam123sam]

Does your VCF file contain depth information (i.e. is there a a DP flag in the FORMAT fields)? If not, it's unlikely that VCFtools will be able to calculate depth.

[Rcucullatus]

Yes, my vcf files have the DP field in the INFO column. That's why I got confused and assumed t was a problem of version incompatibility.

[vivek_]

GATK has a whole suite of walkers that can get info from VCF files.