multiple vcf files to one multisampled vcf file

[Jetse]

Hello everyone,

Does anyone know how I can create one multisampled vcf file of multiple vcf files? Now I have many vcf files which all contain the SNPs of one sample.

Does the program bcftools cat create a multisampled bcf file, or does this one only combine the bcf files?

Or do I have to use samtools mpileup again, now with multiple samples in once?

[xecco]

Try with vcftools vcfmerge (or the improved htscmd)

http://vcftools.sourceforge.net/perl_module.html#vcf-merge

However, if you want a complete sample-specific information on all variant positions, you'll need to re-run mpileup again

[Jetse]

Thanks!
This program looks like it does exactly what I want!

[EDIT]
I used this program for combining the vcf files, but the output is not good enough.
We are going to rerun the samtools mpileup, exactly because the reason you mentioned: the sample-specific information on all variant positions