Error in plotting with vcf compare

Question

[Enrique López]

Hello! I am running vcftools to compare two VCFs, but when I try to plot the results, I have always the same error Use of uninitialized value $out in print at /usr/local/Cellar/vcftools/0.1.15/libexec/bin/vcf-compare line 858.. I revised the line 858: print $fh $out;. The command that I use to run the program is: vcf-compare -p FreeBayes_VT.vcf.gz Manta_VT.vcf.gz. Can somebody help me, please? Thank you!

Answer 1

[Kevin Blighe]

From what I gather, VCFtools is now more or less superceded by BCFtools. Particularly for vcf-compare, you should try bcftools stats, followed by plot-vcfstats for the plotting part.

See also the example on the 'new' VCFtools page: https://vcftools.github.io/htslib.html

Kevin

[Enrique López]

Thanks, I'm using BCFTools and it works!

[Kevin Blighe]

De nada amigo.