Combine all chromosomes in a single file

Question

[bha]

I got 1000 genomes data which is in vcf format. All chromosomes (1 to 22) are in separate files. Is there any way to combine all 22 chromosomes in a single file? My final task is to prune that single file based on MAF and LD. I tried in PLINK (first convert everything in PLINK and tried to merge, but ends up with multi-position variants error, because there are some multiallelics ) . is anyone come across this issue? Any advice please?

[GenoMax]

bcftools merge may be better. Documentation here.

[Bastien Hervé]

Is vcf-tools out of date ?

[bha]

bcftool concat will be more appropriate?

Answer 1

[Bastien Hervé]

To merge vcf you can use vcf-tools merge