How to merge VCF files from multiple samples and remove individual level information

Question

[Arton]

I would like to generate a merged VCF file with variant data (chr, position) from multiple VCF files but remove the individual level information so it can't be traced who has which variant. It's important for me to keep the format as VCF, otherwise this is easily possible if the output was a bed file. For a bed file I use "cut, sort, and uniq". What tool should I use for this purpose to keep the format as VCF but merge all the variants and only keep the unique variants?

[Pierre Lindenbaum]

How to calculate coverage of Nanopore long read data?

Don't forget to follow up on your threads, that is bad etiquette. If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one answer if they all work. If an answer was not really helpful or did not work, provide detailed feedback so others know not to use that answer.

[Arton]

Thank you! Didn't know about these rules. Just accepted the response for the other question.

Answer 1

[Pierre Lindenbaum]

bcftools merge --file-list paths.to.vcfs.txt -O u | bcftools view -G -O z -o output.vcf.gz

[Arton]

Thank you! It worked perfectly.