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#7 Compound heterozygous detection

2.0
closed
Jin Yu
None
2012-12-17
2012-11-19
Anonymous
No

I have been comparing SNP calls from the Illumina platform via ATLAS2 to SNPs in Ion Torrent via my varIONt SNP caller. I find concordance to be generally high, but some of the discordant sites that I find turn out to be compound heterozygous sites where ATLAS calls one allele, and varIONt calls the alternate allele. This seems to be a very rare occurrence (>0.5%), but it is something to think about in the next revision.

Thanks,
Christian.

Discussion

  • Atlas2Team

    Atlas2Team - 2012-11-20
    • status: open --> accepted
     
  • Atlas2Team

    Atlas2Team - 2012-11-26
    • assigned_to: Jin Yu
     
  • Anonymous

    Anonymous - 2012-12-16

    Hi Jin, please close this ticket. I will open another ticket with a more accurate description of the problem. Thanks for your time.
    -Christian.

     
  • Atlas2Team

    Atlas2Team - 2012-12-17
    • status: accepted --> closed
     

Anonymous
Anonymous

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