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Thread: BAM Analysis Kit (Windows and Linux). New release.

  1. #11
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    Quote Originally Posted by teepean47 View Post
    I have released a fix, version 2.0.92. For some reason Git did not update the old executables.

    https://github.com/teepean/BAM-Analysis-Kit/releases
    That works for me. If I gave you a spreadsheet of ISOGG 2017 Y-DNA longhand names would you be able to add them so they show in the output of Complete_SNPs_y.csv? I currently use Access to cross-reference the output so that I can put the SNPs in order by longhand name. The only reason I mention 2017 is because that is closest to what more recent studies have used. Otherwise I would just use the most recent SNP Index that ISOGG has available.

  2. #12
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    Quote Originally Posted by ArmandoR1b View Post
    That works for me. If I gave you a spreadsheet of ISOGG 2017 Y-DNA longhand names would you be able to add them so they show in the output of Complete_SNPs_y.csv? I currently use Access to cross-reference the output so that I can put the SNPs in order by longhand name. The only reason I mention 2017 is because that is closest to what more recent studies have used. Otherwise I would just use the most recent SNP Index that ISOGG has available.
    Sure why not. By the way, Yleaf uses ISOGG from 2019.

  3. #13
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    Quote Originally Posted by teepean47 View Post
    Sure why not. By the way, Yleaf uses ISOGG from 2019.
    Nice. I hadn't looked for YLeaf2 and was used to the first version of YLeaf so I didn't know they had also used a more current tree. I'll get both in the spreadsheet so that we can have both 2019 and 2017 since the 2019 tree has more SNPs.

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    Taking a look at my development bookmarks there are a few things I've saved. These two are written in go so i think getting them working with cygwin isn't out of the question.
    Elprep claims to be a GATK4 replacement https://github.com/ExaScience/elprep
    Bigly is a pileup caller library with more detailed output than the samtools mpileup https://github.com/brentp/bigly

    Only other things I have saved are the mega projects like http://bdgenomics.org/ and https://usegalaxy.org/ which are really impressive but massive projects. There really are some awesome things going on as far as platforms go but even if it's open source it's rarely painless to set up a local version of a hosted platform.

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    I try it and version 2.091 isn´t working. It start analysing, but there is a message sorted a realigned BAM not found. After analysis no SNPs found.

  6. #16
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    Ran 2 more BAMs today, not as successfully.

    I1945 returned as "NA", while I1293 returned just J-CTS5904* (=J2). By comparison, Genetiker reported them as R2a-Y3399 and J2a-CTS1085, respectively.
    "To know nothing of what happened before you were born is to remain forever a child" ― Marcus Tullius Cicero

  7. #17
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    Quote Originally Posted by xenus View Post
    Taking a look at my development bookmarks there are a few things I've saved. These two are written in go so i think getting them working with cygwin isn't out of the question.
    Elprep claims to be a GATK4 replacement https://github.com/ExaScience/elprep
    Bigly is a pileup caller library with more detailed output than the samtools mpileup https://github.com/brentp/bigly

    Only other things I have saved are the mega projects like http://bdgenomics.org/ and https://usegalaxy.org/ which are really impressive but massive projects. There really are some awesome things going on as far as platforms go but even if it's open source it's rarely painless to set up a local version of a hosted platform.
    Elprep looks very interesting and it might speed up the preprocessing stage a bit but unfortunately the actual genotyping is still handled by GATK.

    I have been testing Freebayes but don't have any idea at the moment what settings are suitable for aDNA.

    I did test Bigly but the output was just zeroes for some reason.

  8. #18
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    Quote Originally Posted by AbdoNumen View Post
    Ran 2 more BAMs today, not as successfully.

    I1945 returned as "NA", while I1293 returned just J-CTS5904* (=J2). By comparison, Genetiker reported them as R2a-Y3399 and J2a-CTS1085, respectively.
    Looks like Yleaf doesn't get enough snips to make a prediction. The output of the program Genetiker uses looks very familiar but I do not remember what it is. Anyway he does the prediction "manually".

  9. #19
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    Excellent, thank you! Something seems to be better now.
    The Levänluhta JK2065 individual with the original and the updated analysis kit.
    Here's the Gedmatch comparison differences between the two, and the respective diagnostic statuses.
    This was I believe a sparse DNA set.

    levana.jpg
    Last edited by Puntanen; 06-12-2019 at 11:36 AM.

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

     teepean47 (06-13-2019)

  11. #20
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    Quote Originally Posted by Puntanen View Post
    Excellent, thank you! Something seems to be better now.
    The Levänluhta JK2065 individual with the original and the updated analysis kit.
    Here's the Gedmatch comparison differences between the two, and the respective diagnostic statuses.
    This was I believe a sparse DNA set.
    Increased SNP count is because of a better filter that includes a wider range of SNPs.

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