How to find all SNVs/indels between identical twins (WGS)
Some papers reported using somatic mutation callers (such as Mutect, VarScan) to find the variants between identical twins. It may be not a reasonable approach for these callers are usually used in normal/tumor pair. Any suggestions for that? I would be very grateful for any help!
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samtools mpileupis rapid and great for calling just SNVs. Call them independently in each twin and then compare the calls using custom scripts (e.g. AWK, sed, etc) or by looking here: Best way to compare two samples in a VCF fileI'm struck by the general experimental set-up that you've got, though: