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Thread: Updated BAM Analysis Kit. Any interest?

  1. #1
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    Updated BAM Analysis Kit. Any interest?

    I have been updating Felix' Bam Analysis Kit mainly to speed up the process a bit. My main motivation was to update Samtools as it has gained multi-threading support after Felix released the kit. If there is any interest I can release an updated version to GitHub.

    Updates:

    *Cygwin updated to the latest version

    *Partial Intel GKL support. Multi-threaded PairHMM is not supported as I have not been able to get OpenMP working with MinGW-w64. Compiled with Clang 7.0.0 as GCC's AVX support on Windows is flaky. AVX-512 instructions might be supported but I cannot test it as my CPU does not support them.

    hxxps://github.com/Intel-HLS/GKL

    *Picard updated to the latest version and now includes Intel inflate/deflate from GKL

    *GATK updated to 3.8-1. Includes routines from Intel GKL apart from multi-threaded PairHMM. No support for GATK4 as it does not support RealignerTargetCreator and IndelRealigner. "The indel realignment tools have been retired from the best practices; they are unnecessary if you are using an assembly based caller like Mutect2 or HaplotypeCaller."

    *lobSTR updated to 4.0.6

    *Samtools updated to 1.9. I am currently testing native Windows version vs Cygwin version as native version is considerably faster due to Cygwin's slow file operations. If the output is identical the release will use native version.

    *Java updated to version 8

    Future

    *replace lobSTR with hipSTR

    *use HaploGrep for mtDNA haplogroups. Should be a simple modification as it is a Java command line program

    *experimental Linux version. For some reason chr detection does not work properly on Linux.

    bin\cygwin\bin\bash.exe -c "/bin/samtools.exe view -H bam_complete_sorted.bam|/bin/cut -f2|/bin/grep SN|/bin/grep %%A|/bin/cut -d':' -f2|/bin/head -1 > chr"
    for /F "tokens=1" %%C in (chr) do (bin\cygwin\bin\bash.exe -c "/bin/samtools.exe view -b bam_complete_sorted.bam %%C > chr%%A.bam")

    Problems

    *how to implement hg38 support? Felix did not share how he created some of the references (dbSNP, lobSTR)

    *how to update Y-DNA references?

    *better Y-DNA haplogroup identification. I have tried using 23andme's yhaplo but it does not like VCF format BAM Analysis Kit produces

    hxxps://github.com/23andMe/yhaplo

    *One of the slowest components is gawk but I have no idea how to use Cygwin's anonymous pipes as the Windows native version obviously doesn't support them. How to pipe gzip output to gawk?

  2. The Following 13 Users Say Thank You to teepean47 For This Useful Post:

     anglesqueville (11-03-2018),  Cofgene (11-03-2018),  Eihwaz (11-03-2018),  Erikl86 (11-03-2018),  E_M81_I3A (11-03-2018),  lukaszM (11-03-2018),  MacUalraig (11-03-2018),  Northman (11-03-2018),  poi (11-05-2018),  Robert1 (11-05-2018),  sprfls (11-06-2018),  Waldemar (11-03-2018),  wlk (11-05-2018)

  3. #2
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    R1a > M198 > YP 1337

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    You are a genious. Thanks for that and please share it at Github.

  4. #3
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    R1a > M198 > YP 1337

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    Can you also remove option of sending report from each chromo extraction to if I remember correctly Aws3 or something similar. This step is useless and takes ages sometimes.

  5. #4
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    Quote Originally Posted by lukaszM View Post
    Can you also remove option of sending report from each chromo extraction to if I remember correctly Aws3 or something similar. This step is useless and takes ages sometimes.
    I think that reporting was removed at some point. At least it doesn't mention it any longer.

  6. The Following User Says Thank You to teepean47 For This Useful Post:

     Robert1 (11-09-2018)

  7. #5
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    A release on GitHub would be great. I agree with Lukasz, teepean47 you are a genius and our benefactor.
    En North alom, de North venom
    En North fum naiz, en North manom

    (Roman de Rou, Wace, 1160-1170)

  8. #6
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    Sounds good. I am up!

  9. #7
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    Felix's BAM analysis kit produces biased calls, so that samples analyzed with this setup aren't compatible with the academically released genotypes, so I'm not sure what the excitement is about?

    Fix this problem and then yeah, I'll be excited as well.

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     Vadim Verenich (11-20-2018)

  11. #8
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    Quote Originally Posted by Generalissimo View Post
    Felix's BAM analysis kit produces biased calls, so that samples analyzed with this setup aren't compatible with the academically released genotypes, so I'm not sure what the excitement is about?

    Fix this problem and then yeah, I'll be excited as well.
    What is a biased call?

  12. #9
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    removed
    Last edited by teepean47; 11-03-2018 at 05:57 PM. Reason: Apparently I cannot delete posts.

  13. #10
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    Quote Originally Posted by Generalissimo View Post
    Felix's BAM analysis kit produces biased calls, so that samples analyzed with this setup aren't compatible with the academically released genotypes, so I'm not sure what the excitement is about?

    Fix this problem and then yeah, I'll be excited as well.
    Can you post any examples of biased calls?

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