How to transform a whole-genome callset into whole-exome callset?

How to transform a whole-genome callset into whole-exome callset?

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Hi all,

I have a callset from whole-genome data and with this callset, I want to transform it into exome callset by extracting the variants using a exome target interval. I obtained two exome target list, one from 1KG project (Phase 3) and the Twist Exome target (www.twistbioscience.com/resources/bed-file/ngs-human-core-exome-panel-bed-files). I have some questions:

  • Are these exome intervals appropriate to get the exon variants? If so, which one should I use? I subset my VCF file with both lists and for 1KG I got 68463 variants while with Twist Exome target, I got 21082.
  • Looking at the annotations for the subset (regardless if it was with 1KG or Twist), I get variants annotated as introns even if they are tagged as protein coding transcripts. Does this makes sense for an exome target list?

Thank you very much for your help!

Kind regards,

Alejandro


calling


wes


variant


wgs

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