VCF_operations.md

Some common operations on VCF files

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Look at a specific portion of a VCF file in the terminal using tabix and less

tabix file.vcf.gz {chr}:{start}-{stop} | less -S

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Extract a specific portion of a VCF file and write to a new file using tabix & bgzip, including the header from the old file. Useful if you want a small file for testing on...

tabix input.vcf.gz -h {chr}:{start}-{stop} | bgzip > outfile.vcf.gz; tabix outfile.vcf.gz

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Get the sample names from a VCF file

bcftools query -l file.vcf.gz

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View the header only

bcftools view -h file.vcf.gz

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Subset a ~VCF file by samples

bcftools view -Oz -S samples.txt INFILE > OUTFILE.vcf.gz