Alsayari

Dear All,

First i would like to congratulate the Dantelabs for opening this forum fo the users which is a good medium to discuss and find information as well as suggest features that will enhance user benefits.    


now for the real topic. I would like to know why did Dantelabs .bam files use Hg19 coding even thought Hg38 is available since 2013 pointing that the lab is state if the art lab and have just been built.
 

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matt
Hey Alsayari, 

Thanks for your question.

We currently use the GRCh37 reference as this is the most ubiquitous reference used for consumer genomics services (for example, the probe set used by 23andMe) and therefore more tools oriented towards consumers provide support for GRCh37/HG19 aligned samples than GRCh38/hg38. However, we appreciate that there is a demand at the moment for GRCh38 output so we'll be offering this to consumers very soon, directly through the Genome Manager interface.

Matt
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Petr
Do you mean something different than https://www.dantelabs.com/products/alignment-to-the-grch38 ?
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matt
Yep! It will be a slightly more integrated solution that requires less intervention on our side meaning that you will get you your new results faster
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anorris8
A lot of the genomics field still uses hg19 because of the rich annotation available for hg19 compared to hg38. There is a shift now to hg38 with more annotation becoming available. You can use UCSC liftover tool for specific genomic coordinates.
I don't suggest doing liftover on your entire vcf file because it's imperfect. It's better to re-align your raw data to hg38. It's possible that you could use a cloud computing resource to do this (precisionFDA, Galaxy, etc.).
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