Anca1983
What are the beat programs or websites to convert WGS file into 23 and me file type for 3rd party websites?
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massmanute
I have a similar question. However, in addition to 23&me format, I would also like to be able to convert to ftdna format and Ancestrydna format.
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Petr
Probably WGSExtract https://dnagenics.com/adn/wgs-extract-bam-file-fastq/ is the best - very easy to use, for Windows/Linux/Mac, many output formats.
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Falko
However be aware not to use WGSExtract data for health related purposes, the data is only suitable for Genealogy as it does not process indels in the correct way...
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Petr
Yes, indels are processed incorrectly, but more than 90 % of health related SNPs are not indels. But there is another thing - 30x coverage is an average, but some SNPs may have much lower coverage and then the result is not reliable enough.
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Falko
Yap, just wanted to make people aware that the indels will cause false positives in many health reporting tools.
This could scare someone who is not aware of this limitation.
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Petr
You are right, I was really surprised by the first Promethease report based on WGSExtract data. I was able to create complete list of 23andMe indels but I don't know how to incorporate it to the extract23 script.
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Umesh Reclusa hominid indica
Anyone has found a way to analyse Dante Labs Data on Promethease? The WGS Extract Indel issue still persists?
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Clare86
You can upload both the snp and indel vcf files to promethease.

Another option would be to use sequencing.com to create a genome vcf file which contains genotypes for all positions and then upload that. 

Indels are a bit difficult anyway. I uploaded my vcf files to Varsome Pro and then started cross checking anything interesting with my Sano Genetics and Nebula Genomics data. A lot of them were only present in the Dante data.
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Umesh Reclusa hominid indica
Thanks for the prompt reply. 🙂
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Randy H
The indel is a bigger issue than just WGS Extract handling.  The vendors themselves do not treat the InDels the same.  Ancestry, 23andMe, FamilyTreeDNA and LivingDNA report the "same" InDels differently.  As was mentioned by Clare, the InDel files from Nebula, Dante and Sano are different because they are using different pipelines and filters.  It is a bit of a mess and something not easily fixed until a single, standard way of identifying and reporting them is made. And then the microarray companies conform.  Or, at best, coming up with that definition and then running a filter on existing microarray files to try and transform them to a common form.
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