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Thread: Dante Labs (WGS)

  1. #781
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    Should probably start (another) thread on genomics security. The hard-drive/USB-key home-delivery is probably worst possible choice from security standpoint. In my case, the courier/deliveryman handed it out to me with no identification or verification while I was just standing outside. There is also fairly good chance that mysterious storage-media gets copied for analysis at each border-crossing. Also, anybody else at the receiving household will have access to it, which may not be desirable in many cases. The way to do the transfer safely is to encrypt the media with strong encryption, and provide the encryption key on the web-site to authenticiated user. Of course, encryption isn't always user-friendly, so perhaps make it optional.

    HTTPS transfers itself are fairly secure, I'd like to say, as secure as we know to make them, the risks to online-transfer are mainly related to endpoints, including someone getting copy of the company's SSL/TLS certificate, but in that case they can probably get a copy of the data as well. I'm not sure if there are any DTC genomic companies where genetic data is NEVER loaded on Internet-connected computer. The relative risk of WGS vs. microarray would be a fascinating debate, if a BAM file is around 100GB compressed and often ambiguous while requiring non-trivial computing resources, it becomes somewhat self-limited compared to microarray files. Nevertheless, microarrays (AncestryDNA, MyHeritage, 23andMe etc.) are more than enough to identify people, their genetic ethnicity, and genetic variants of known effect.

    Consent is extremely important for reasons of ethics, trust and people's feeling of agency. However, please remember that there are many genetic analysis labs that will analyze samples no questions asked, or you can just say it's your late father's chewing gum for genealogical research. VolTRAX + Flongle even today allows DNA sequencing on the fly with a mobile phone. It's been shown time and time again that's it's far more cost-effective and succesful to just re-sequence someone's genome than to obtain it via targeted hacking. Researchers have access to hundreds of thousands of sequenced samples with attached information about ethnicity, medical conditions etc. so they're not really interested in obtaining YOUR sample with no attached information. Some opportunistic hacks like indeed having a program that copies your genotypes & contents of Documents folder, or blackmailing a company by threatening to reveal customer's genetic information are likely, and with more people taking genetic tests, scams claiming to have your genetic data can't be far behind, and will cause some issues.

  2. #782
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    How long you were waiting for results?

  3. #783
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    I seriously give up. Using EvE, using WGS Extract, using DNA Kit Studio or whatever - I still can't get a normal raw data file to upload to GEDmatch or to use in Global25 (Davidski got bogus results).

    For now, I'm happy with the YFull upload I got and the full medical report I have.

    I did manage to get nice results through GEDmatch by merging my DanteLab's 23andMe extraction upload with my previous 23andMe v5 upload, but it just seems to rely mostly on my v5 upload - but it just seems to not be usable in ancestry testing yet, unfortunately.
    Check out my Hidden Content
    My Y-DNA: Q-M242 -> Q-L232 -> Q-L275 -> Q-M378 -> Q-Y2016 -> Q-L245 -> Q-FGC1904 -> Q-Y2209 -> Q-Y2225 -> Q-Y2197 -> Q-Y2750 -> Q-YP1004 -> Q-YP3924;
    My mtDNA: K1a1b1a;

    My dad's mtDNA: K2a2a;

  4. #784
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    Quote Originally Posted by Erikl86 View Post
    I seriously give up. Using EvE, using WGS Extract, using DNA Kit Studio or whatever - I still can't get a normal raw data file to upload to GEDmatch or to use in Global25 (Davidski got bogus results).
    I got ok results with EvE by converting FASTQ -> gVCF hg19 and then running DNA Kit Studio on it with Livingdna template.

  5. #785
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    Quote Originally Posted by Erikl86 View Post
    I seriously give up. Using EvE, using WGS Extract, using DNA Kit Studio or whatever - I still can't get a normal raw data file to upload to GEDmatch or to use in Global25 (Davidski got bogus results).
    [...]
    I did manage to get nice results through GEDmatch by merging my DanteLab's 23andMe extraction upload with my previous 23andMe v5 upload, but it just seems to rely mostly on my v5 upload - but it just seems to not be usable in ancestry testing yet, unfortunately.
    Did WGSExtract show you an error message in the black command line window? If an error occures, than an empty 23andme file is produced.
    The downloadable beta version had the following limitations:

    - the .bai index file had to be in the same directory as the bam file
    - the path of the bam file wasn't allowed to have non standard characters in it
    - autosomal export was only possible for hg19

    The next version addresses these issues, but it is not published yet.

  6. The Following User Says Thank You to mwasser For This Useful Post:

     Erikl86 (06-13-2019)

  7. #786
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    Quote Originally Posted by tontsa View Post
    I got ok results with EvE by converting FASTQ -> gVCF hg19 and then running DNA Kit Studio on it with Livingdna template.
    Awesome ! I'll try to use the LivingDNA template !

    EDIT: Didn't work - got the same bogus results
    Last edited by Erikl86; 06-13-2019 at 09:28 AM.
    Check out my Hidden Content
    My Y-DNA: Q-M242 -> Q-L232 -> Q-L275 -> Q-M378 -> Q-Y2016 -> Q-L245 -> Q-FGC1904 -> Q-Y2209 -> Q-Y2225 -> Q-Y2197 -> Q-Y2750 -> Q-YP1004 -> Q-YP3924;
    My mtDNA: K1a1b1a;

    My dad's mtDNA: K2a2a;

  8. #787
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    Quote Originally Posted by mwasser View Post
    Did WGSExtract show you an error message in the black command line window? If an error occures, than an empty 23andme file is produced.
    The downloadable beta version had the following limitations:

    - the .bai index file had to be in the same directory as the bam file
    - the path of the bam file wasn't allowed to have non standard characters in it
    - autosomal export was only possible for hg19

    The next version addresses these issues, but it is not published yet.
    I just saw that FullGenomes have forgot to provide me with the .bai file for the realigned hg19 bam file.
    Check out my Hidden Content
    My Y-DNA: Q-M242 -> Q-L232 -> Q-L275 -> Q-M378 -> Q-Y2016 -> Q-L245 -> Q-FGC1904 -> Q-Y2209 -> Q-Y2225 -> Q-Y2197 -> Q-Y2750 -> Q-YP1004 -> Q-YP3924;
    My mtDNA: K1a1b1a;

    My dad's mtDNA: K2a2a;

  9. #788
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    The next, yet unpublished version of WGSExtract checks directly after opening a bam file if there is no .bai index file, and creates it in that case.
    In the meantime, there is an alternative possibility to create it, albeit a bit more cumbersome:
    If you don't feel uncomfortable using the windows command line, you could open the command line, go to the "samtools-cygwin" subdirectory of WGSExtract, and type:
    samtools index /path/to/your/bamfile/filename-of-bamfile.bam
    This would create the missing .bai index file.

  10. The Following User Says Thank You to mwasser For This Useful Post:

     Erikl86 (06-13-2019)

  11. #789
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    Quote Originally Posted by mwasser View Post
    The next, yet unpublished version of WGSExtract checks directly after opening a bam file if there is no .bai index file, and creates it in that case.
    In the meantime, there is an alternative possibility to create it, albeit a bit more cumbersome:
    If you don't feel uncomfortable using the windows command line, you could open the command line, go to the "samtools-cygwin" subdirectory of WGSExtract, and type:
    samtools index /path/to/your/bamfile/filename-of-bamfile.bam
    This would create the missing .bai index file.
    I get this comment when I run it:

    "[W::bam_hdr_read] EOF marker is absent. The input is probably truncated"
    Check out my Hidden Content
    My Y-DNA: Q-M242 -> Q-L232 -> Q-L275 -> Q-M378 -> Q-Y2016 -> Q-L245 -> Q-FGC1904 -> Q-Y2209 -> Q-Y2225 -> Q-Y2197 -> Q-Y2750 -> Q-YP1004 -> Q-YP3924;
    My mtDNA: K1a1b1a;

    My dad's mtDNA: K2a2a;

  12. #790
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    Ok so I ran WGSExtract now with my bai file, and I get 1 kb size raw data file - which means a bogus file.

    This is what I get:

    CWGSExtractBeta\WGSExtract\programs\wgsextract>"CWGSExtractBeta\WGSExtract\programs\samtools-cygwin\bash" "CWGSExtractBeta\WGSExtract\temp\extract23.sh"
    bash.exe: warning: could not find /tmp, please create!
    Starting mpileup... Please be patient!
    [warning] samtools mpileup option `v` is functional, but deprecated. Please switch to using bcftools mpileup in future.
    [mpileup] 1 samples in 1 input files
    Mpileup completed. Starting SNP calling...
    Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
    SNP calling completed. Starting annotation...
    Annotation completed. Starting extraction from VCF ...
    Extraction from VCF completed. Sorting by chromosome and position ...
    dos2unix: converting file C:/BAM/output/ASJ9N.GRCh37__23andmeV3.txt to Unix format...
    C:/BAM/output/ASJ9N.GRCh37__23andmeV3.txt was created. Compressing ...
    adding: ASJ9N.GRCh37__23andmeV3.txt (deflated 46%)
    extract23: Output file C:/BAM/output/ASJ9N.GRCh37__23andmeV3.txt.zip was created.
    Check out my Hidden Content
    My Y-DNA: Q-M242 -> Q-L232 -> Q-L275 -> Q-M378 -> Q-Y2016 -> Q-L245 -> Q-FGC1904 -> Q-Y2209 -> Q-Y2225 -> Q-Y2197 -> Q-Y2750 -> Q-YP1004 -> Q-YP3924;
    My mtDNA: K1a1b1a;

    My dad's mtDNA: K2a2a;

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