merging individuals vcf.gz files to one vcf file in linux
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
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Pierre Lindenbaum
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mozduri •
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mozduri •
1 answer
Bcftools index doesnt work with multiple files. You ll have to invoke bcftools index for each individual vcf
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