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Thread: Dante Labs (WGS)

  1. #261
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    I believe you can get it in hg19 or hg38 if you ask for it. That's based on some comments here on the technical thread and this on their website:

    'We offer variant calling against hg19 (GRCh37) or hg38 (GRCh38), depending on the customers' needs.'

    There have been YFull submissions in both. If someone asked for hg38 recently and was declined please correct me.
    YSEQ:#37; YFull: YF01405 (Y Elite 2013)
    GEDMatch: A828783 (autosomal DNA), 9427684 (GEDCOM) for segment matching DO NOT POST ADMIXTURE REPORTS USING MY KIT
    WGS (Full Genomes Nov 2015)
    Ancestry GCs: Scots in central Scotland & Ulster, Ireland; English in Yorkshire & Pennines
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  2. #262
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    U3a1c1

    Catalonia Andorra Gibraltar
    Gedmatch Genesis rejected 5 times my Dantelabs WGS snp.VCF uploading. Finally, I worked with Beagle 4.1 (without map, default settings: 1 cM/1 Mb) to generate a lighter VCF (only 18 Mb compressed by bgzip). New kit NY6801335 matches perfectly to my 23andme kit and my father's GFG. Only my Gencove imputed VCF shares less percentage, about 98%

  3. #263
    Quote Originally Posted by Miqui Rumba View Post
    Gedmatch Genesis rejected 5 times my Dantelabs WGS snp.VCF uploading. Finally, I worked with Beagle 4.1 (without map, default settings: 1 cM/1 Mb) to generate a lighter VCF (only 18 Mb compressed by bgzip). New kit NY6801335 matches perfectly to my 23andme kit and my father's GFG. Only my Gencove imputed VCF shares less percentage, about 98%
    Gedmatch Genesis accepts only hg19 while my vcf is in hg38, is there any way to convert it?

  4. #264
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    Catalonia Andorra Gibraltar
    Yes, you can convert human references with liftover tool, it is free in UCSC and Ensembl webs though I prefer usegalaxy.org platform because I can filter and normalize SNPs with another programs (picard tools, bcftools). However, we must collaborate to make an standard genealogic pattern, collecting only SNPs wich accepts Gedmatch genesis and Eurogenes calculators. Genesis processed 1.8M SNPs from 3.5M total SNPs and selected only about 500,000 SNPs. When I ran Eurogenes k36 calculator in chromosome view I've seen that only chroms 1,2 and 3 have thousands of SNPs selected, the rest 1 o 0 SNPs (impossible to get results). MDLP calculators run better results for WGS kits.

  5. The Following 2 Users Say Thank You to Miqui Rumba For This Useful Post:

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  6. #265
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    T1a1j

    Sweden
    I read that YSEQ provides a special vcf file with their WGS test, a file that includes the SNPs used in versions 2-5 of the 23andme chips. That should give good matching to all autosomal products except maybe the new Ancestry V2 test.

  7. #266
    Quote Originally Posted by Miqui Rumba View Post
    Yes, you can convert human references with liftover tool, it is free in UCSC and Ensembl webs though I prefer usegalaxy.org platform because I can filter and normalize SNPs with another programs (picard tools, bcftools). However, we must collaborate to make an standard genealogic pattern, collecting only SNPs wich accepts Gedmatch genesis and Eurogenes calculators. Genesis processed 1.8M SNPs from 3.5M total SNPs and selected only about 500,000 SNPs. When I ran Eurogenes k36 calculator in chromosome view I've seen that only chroms 1,2 and 3 have thousands of SNPs selected, the rest 1 o 0 SNPs (impossible to get results). MDLP calculators run better results for WGS kits.
    Thank you! Platform usegalaxy.org looks nice, I am going to learn how to use it. Unfortunately, I am new in this.

  8. #267
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    Dante Labs Black Friday sale is now on, 169 Euros for a WGS test!


    My Full DNA: Whole Genome Sequencing with mtDNA
    €169.00 EUR €850.00 EUR You save €681.00 EUR

    https://www.dantelabs.com/products/w...ome-sequencing
    YSEQ:#37; YFull: YF01405 (Y Elite 2013)
    GEDMatch: A828783 (autosomal DNA), 9427684 (GEDCOM) for segment matching DO NOT POST ADMIXTURE REPORTS USING MY KIT
    WGS (Full Genomes Nov 2015)
    Ancestry GCs: Scots in central Scotland & Ulster, Ireland; English in Yorkshire & Pennines
    Hidden Content

  9. The Following 4 Users Say Thank You to MacUalraig For This Useful Post:

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  10. #268
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    Quote Originally Posted by MacUalraig View Post
    Dante Labs Black Friday sale is now on, 169 Euros for a WGS test!
    Question though, how much better is their GenomeZ version? I was hoping that would be taken down a couple hundred dollars but it's never on sale. I'm fairly new to sequencing and trying to learn technical terms. So far it looks like that test has higher resolution exome sequencing? Is there something I'm missing? There is a huge price gap between the two tests, even when not on sale. Dante Labs also said they were working on long read sequencing 7 days ago. If that is even better, would it be worth waiting for?
    Last edited by lnight; 11-18-2018 at 09:25 PM.

  11. #269
    Quote Originally Posted by MacUalraig View Post
    Dante Labs Black Friday sale is now on, 169 Euros for a WGS test!


    My Full DNA: Whole Genome Sequencing with mtDNA
    €169.00 EUR €850.00 EUR You save €681.00 EUR
    At this price, we should add an additional fee €59 for fard disc that contains FASTQ and BAM files.

    So for people who wish Yfull analysis price is actually 169+59=228€
    Anyway, I think this is currently the cheaper WGS.

  12. #270
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    Quote Originally Posted by lnight View Post
    Question though, how much better is their GenomeZ version? I was hoping that would be taken down a couple hundred dollars but it's never on sale. I'm fairly new to sequencing and trying to learn technical terms. So far it looks like that test has higher resolution exome sequencing? Is there something I'm missing? There is a huge price gap between the two tests, even when not on sale. Dante Labs also said they were working on long read sequencing 7 days ago. If that is even better, would it be worth waiting for?
    Yes the Z version does high read sequencing of the exome at 130x then 30x for the rest of the genome. Depends on your budget and how interested you are in the autosomal data (eg health related information). If you are only interested in a cheap route to a Y sequencing stick with the cheaper version since it will be the same coverage, except of course for a sprinkling of genes on the Y which would be covered at greater depth.
    YSEQ:#37; YFull: YF01405 (Y Elite 2013)
    GEDMatch: A828783 (autosomal DNA), 9427684 (GEDCOM) for segment matching DO NOT POST ADMIXTURE REPORTS USING MY KIT
    WGS (Full Genomes Nov 2015)
    Ancestry GCs: Scots in central Scotland & Ulster, Ireland; English in Yorkshire & Pennines
    Hidden Content

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