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  #1  
Old 1st March 2018, 05:30 PM
JohnInMass JohnInMass is offline
FTDNA Customer
 
Join Date: Feb 2018
Posts: 3
BigY download of csv file

My biggest pet peeve is with the BigY download (the csv file option).

For KnownSNP, for some reason FTDNA decides to leave the position field blank for named SNPs. For the Novel Variant, the position field is filled in.

Why is this an issue? Many of the derived state = NO include low quality reads. One needs to examine each SNP to find the position number, and then visually review the detail to find low quality reads. This would be far simpler if the position field for known snps was filled in, and linkage could occur to other sources of data quality (vcf for one).

Many of the SNPs are not in an external database (such as the one from Ybrowse), for my kit I'm counting in excess of 4500. Of my 90,000 plus known snps, I can equate the known snps to the snpname from ybrowse for all but these 4500.

For Snps in derived state = ?, there are instances of zero reads which is also handy to know--since I cannot find these in the vcf file.

I think it would be a good idea to add position to the csv file download option for Known Snps.

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  #2  
Old 2nd March 2018, 09:21 AM
John McCoy John McCoy is offline
FTDNA Customer
 
Join Date: Nov 2013
Posts: 692
Excellent idea! Should be an easy fix if/when a programmer is actually given the task. Having both the SNP name and the position should resolve the confusions that can easily arise with SNP's that are not well known or that someone has transcribed incorrectly in an email. The position plus the SNP name will make it easier to spot the inevitable typos.
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  #3  
Old 2nd March 2018, 11:22 AM
dtvmcdonald dtvmcdonald is offline
mtDNA: | Big Y Pending
 
Join Date: Mar 2011
Posts: 264
This is an old gripe. Its been reported ad nauseum. I sent
a scathing request to fix this the Bennett himself.
I'm admin of one of the top 3 surname projects, wrote the
original Pop Finder, and we've personally met a few times. He actually replied ... but no progress.

This is probably the #1 most egregious gripe. They MUST know those numbers.
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