Compare mutations between two samples

[BjoerlingTaul]

how to compare mutations between two matched samples?

For example: If you want to identify SNPs in one sample relative to another sample (for example, if you sequenced your lab wild-type strain and want to find out mutations relative to this wild-type).

[apetkau]

If you wanted to operate directly on the VCF files you could use bcftools isec: https://samtools.github.io/bcftools/bcftools.html#isec