Question: How to find all SNVs/indels between identical twins (WGS)
gravatar for hqyang2
20 months ago by
hqyang20 wrote:

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!

sequencing snp genome • 502 views
ADD COMMENTlink written 20 months ago by hqyang20

samtools mpileup is 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 file

I'm struck by the general experimental set-up that you've got, though:

  • From which tissue did you derive your sample?
  • Are these monozygotic twins?
ADD REPLYlink written 20 months ago by Kevin Blighe49k
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