Variant calling

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Data analysis

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We now have SNPs in variants.bcf and variants2.bcf.

We want those SNPs to end up in the right genomic order, so let’s use the bcftools merge command:

bcftools merge variants.bcf variants2.bcf > combined.vcf

Inspect the values in the POS column to make sure they are in the right order:

bcftools view combined.vcf