merging individuals vcf.gz files to one vcf file in linux

Question

[mozduri]

Hello everyone I have animals imputed sequence wide genotypes from SkimSEEK (Low pass). I want merge all individuals together in VCF. I run bellow code but I get error: bcftools merge file1.vcf.gz file2.vcf.gz file3.vcf.gz .... -Oz -o merged4.vcf.gz

failed to open:could not load index

then I generate index with bellow code and I get this error: bcftools index *.vcf.gz failed to open:could not load index

What is the problem?

Regards Zohre

Answer 1

[Pierre Lindenbaum]

Bcftools index doesnt work with multiple files. You ll have to invoke bcftools index for each individual vcf