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Thread: Updated BAM Analysis Kit. Any interest?

  1. #81
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    Quote Originally Posted by teepean47 View Post

    1) How does one use pileupCaller? It mentions "Eigenstrat positions file" but at which point is that created and from what data?
    EIGENSTRAT position file can be easily generated by a simple AWK command.

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    Quote Originally Posted by Vadim Verenich View Post
    I am interested in benchmarking the full process of conversion from FASTQ to VCF
    I analyzed JK1970 with default settings using WSL. The process started at 7:10 and VCF was created 8:53. Reference was already indexed by BWA. I can time it properly if you want.


    ftp://ftp.sra.ebi.ac.uk/vol1/fastq/E...57057.fastq.gz
    Last edited by teepean47; 12-03-2018 at 09:02 PM.

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

     Vadim Verenich (12-04-2018)

  4. #83
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    Quote Originally Posted by Vadim Verenich View Post
    EIGENSTRAT position file can be easily generated by a simple AWK command.
    From which data? If I have a BAM or a FASTQ and I want to run pileupCaller I have no idea how to create the needed EIGENSTRAT posititions file.

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    Quote Originally Posted by teepean47 View Post
    From which data? If I have a BAM or a FASTQ and I want to run pileupCaller I have no idea how to create the needed EIGENSTRAT posititions file.
    pileupCaller would work with pileup only, so first of all you need to generate pileup from BAM files using this command

    samtools mpileup -R -B -q30 -Q30 -l <list_of_positions.txt> \
    -f <reference_genome.fasta> > genome.pileup
    Th next step would be:

    cat genome.pileup | pileupCaller --sampleNames Sample1,Sample2,Sample3 \
    --samplePopName MyPop -f <Eigenstrat.snp> \
    -o EigenStrat -e <My_output_prefix>
    Eigenstrat positions file is just a plain text format (Eigenstrat SNP file format)

    rs3094315 1 0.007526 752566 G A
    rs7419119 1 0.008420 842013 G T
    rs13302957 1 0.008910 891021 G A
    rs6696609 1 0.009034 903426 T C
    rs8997 1 0.009497 949654 A G
    rs9442372 1 0.010187 1018704 A G
    rs147606383 1 0.010453 1045331 A G
    rs4970405 1 0.010490 1048955 G A
    rs11807848 1 0.010612 1061166 C T
    rs4970421 1 0.011086 1108637 A G
    rs1320571 1 0.011204 1120431 A G
    rs2887286 1 0.011561 1156131 C T
    rs79118541 1 0.011575 1157547 C T
    rs3813199 1 0.011583 1158277 A G
    rs113791678 1 0.011618 1161780 T C
    rs78424188 1 0.011706 1170587 T C
    rs12073590 1 0.012052 1205155 C A
    rs6685064 1 0.012113 1211292 T C
    If you don't know how to generate this format from PLINK bim file, then I would suggest using any SNP file in Eigenstrat format (you can download them from David Reich Lab's Datasets)

  6. #85
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    Quote Originally Posted by teepean47 View Post
    I can use them either with WSL or with Cygwin.
    I just saw your reply. Will send tonight

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    Quote Originally Posted by teepean47 View Post
    I can use them either with WSL or with Cygwin.
    Just sent you a simple script to pull rs IDs from a 4 million position text file into your VCF.

  8. #87
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    This seems like the proper place to ask this.

    I have aDNA sample of a 4th-1st century BC Phoenician from Matisoo-Smith et al. (2018).

    It's in FASTAQ format - roughly ~650 MB zipped.

    Can anyone here please provide a route for converting it into a VCF? Or convert it and send a link for download, here's the FASTAQ file:

    https://drive.google.com/open?id=19J..._rY-h-XAQ_b478
    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. #88
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    Quote Originally Posted by Erikl86 View Post
    This seems like the proper place to ask this.

    I have aDNA sample of a 4th-1st century BC Phoenician from Matisoo-Smith et al. (2018).

    It's in FASTAQ format - roughly ~650 MB zipped.

    Can anyone here please provide a route for converting it into a VCF? Or convert it and send a link for download, here's the FASTAQ file:

    https://drive.google.com/open?id=19J..._rY-h-XAQ_b478
    I could try to convert this file

  10. #89
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    Quote Originally Posted by Vadim Verenich View Post
    I could try to convert this file
    Unfortunately, it's just mitochondrial genome
    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;

  11. #90
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    Here's my first test run with pileupCaller. Anyone want to check the results? They are in plink format. I used BOO006 from Levšnluhta.

    https://drive.google.com/open?id=1BI...aqPW5bC9LLnc_6

    https://www.ebi.ac.uk/ena/data/view/PRJEB29360

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