Thanks, I'm using BCFTools and it works!
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Enrique López •
Error in plotting with vcf compare
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!
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Kevin Blighe
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Enrique López •
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Enrique López •
1 answer
From what I gather, VCFtools is now more or less superceded by BCFtools.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
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Kevin Blighe
De nada amigo.
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