#7 Compound heterozygous detection

[Anonymous]

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.

[Anonymous]

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