combining samples from different platforms

erikenpeererikenpeer AmsterdamMember

Hi,

We have a total of 5 exomes from 1 family. 3 of the exomes are sequenced at sanger and 2 at BGI. My first thought was to recall the variants for all 5 exomes at once. Doing this gives me a error message about the contigs. What would be the best way to recall the 5 samples at once? I have the .bam files from the 5 exomes.

best,

Erik

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi Erik,

    Can you post the error message you get? My guess is that your exomes were aligned against different versions of the reference. If so, to call them together you'll need to realign one of the sets to match the rest.

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