How to get GQ after running BCFTools?
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6.8 years ago
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New version of BCFTools (using call instead of view) doesn't produce VCF files with GQs in the FORMAT field.

Does anyone know how to get it in the new version (1.1)?

sequencing SNP • 2.3k views
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4
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6.6 years ago

When you run bcftools call specify -f GQ to have it added to the output

 bcftools call -vmO z -f GQ
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