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Combine all chromosomes in a single file

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?

genetics
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updated by Bastien Hervé Bastien Hervé • written by bha bha

bcftools merge may be better. Documentation here.

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written by GenoMax GenoMax

bcftool concat will be more appropriate?

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written by bha bha

1 answer

To merge vcf you can use vcf-tools merge

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written by Bastien Hervé Bastien Hervé

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