Extract variants/SNPs with T>G substitution from a VCF file
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16 months ago
Nanu • 0

Is there a way to extract all variants/SNPs in a VCF file that have a T>G change across all chromosomes ? I'm looking at bcftools but but unable to find any filtering options for REF/ALT.

Thank you

VCF SNP • 576 views
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Entering edit mode
16 months ago
4galaxy77 2.8k

Use bcftools view with the -i flag for including variants.

bcftools view -i'REF=="T" & AlT == "G"'
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