Doug, I take you point, however, the new tools, by colour density, attempt to advise, High, Medium or Low quality.  As you say, lets see the actual revised BAM files. Cheers *Dennis Wright* // On 14/10/2017 10:23 AM, McDonald, J Douglas wrote: > Yes, and what fraction of those will turn out to be wrong or useless? > > Look where they are. When the BAMs arrive, look at their mapping quality! > > Doug McDonald > ________________________________________ > From: GENEALOGY-DNA [[email protected]] on behalf of Dennis Wright [[email protected]] > Sent: Friday, October 13, 2017 5:14 PM > To: R1b-L21 Yahoo Groups; Rootsweb Genealogy DNA > Subject: [DNA] HG38 Results are revealing additional SNPs > > It appears that in the new Big-Y result pages that are slowly coming > through, the 'unnamed variants' are indeed new, and not recognised in > the earlier hg19 VCF/BAM files. > > The new tools are very workable, and perhaps there is less need for our > detailed analysis ... time will tell. > > -- > *Dennis Wright* > > > ------------------------------- > To unsubscribe from the list, please send an email to [email protected] with the word 'unsubscribe' without the quotes in the subject and the body of the message > > > ------------------------------- > To unsubscribe from the list, please send an email to [email protected] with the word 'unsubscribe' without the quotes in the subject and the body of the message >

I think they mean high BASE call quality. That's meaningless if the reads are in the wrong place and your base is correct at the correct spot. This has long been a terrible problem ________________________________________ From: GENEALOGY-DNA [[email protected]] on behalf of Dennis Wright [[email protected]] Sent: Friday, October 13, 2017 6:37 PM To: [email protected] Subject: Re: [DNA] HG38 Results are revealing additional SNPs Doug, I take you point, however, the new tools, by colour density, attempt to advise, High, Medium or Low quality. As you say, lets see the actual revised BAM files. Cheers *Dennis Wright* // On 14/10/2017 10:23 AM, McDonald, J Douglas wrote: > Yes, and what fraction of those will turn out to be wrong or useless? > > Look where they are. When the BAMs arrive, look at their mapping quality! > > Doug McDonald > ________________________________________ > From: GENEALOGY-DNA [[email protected]] on behalf of Dennis Wright [[email protected]] > Sent: Friday, October 13, 2017 5:14 PM > To: R1b-L21 Yahoo Groups; Rootsweb Genealogy DNA > Subject: [DNA] HG38 Results are revealing additional SNPs > > It appears that in the new Big-Y result pages that are slowly coming > through, the 'unnamed variants' are indeed new, and not recognised in > the earlier hg19 VCF/BAM files. > > The new tools are very workable, and perhaps there is less need for our > detailed analysis ... time will tell. > > -- > *Dennis Wright* > > > ------------------------------- > To unsubscribe from the list, please send an email to [email protected] with the word 'unsubscribe' without the quotes in the subject and the body of the message > > > ------------------------------- > To unsubscribe from the list, please send an email to [email protected] with the word 'unsubscribe' without the quotes in the subject and the body of the message > ------------------------------- To unsubscribe from the list, please send an email to [email protected] with the word 'unsubscribe' without the quotes in the subject and the body of the message