I have a freebayes genotyped multisample vcf file. I want to sort the names of the samples in alphabetical order to make my life a bit easy with post variant calling analysis. I have tried Picared SortVcf which work fine which works fine on a small file but failed on a large file (~4 Gb). If you suggest ways to sort a large multi-sample file without distorting the variants information, it would a great help.
Hey, try this:

    $ bcftools query -l input.vcf | sort > samples.txt
    $ bcftools view -S samples.txt input.vcf > output.vcf


If not already done, I would also suggest to use `bcf` instead of `vcf` or `vcf.gz`. This really improves speed when working with `bcftools` on large datasets.

fin swimmer