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Thread: Updated BAM Analysis Kit. Any interest?

  1. #101
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    Quote Originally Posted by teepean47 View Post
    Sure. I still have the problem with rs-values disappearing during the process. I recently got a new job and haven't had the time to investigate the issue.
    I don't need the rs values.

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  3. #102
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    Quote Originally Posted by Generalissimo View Post
    I don't need the rs values.
    I would like to keep them and I would like to know what is causing that.

    I had time to process the first one, PG2001.

    https://drive.google.com/open?id=1hv...Qg7KAyewO6XX3o
    Last edited by teepean47; 01-21-2019 at 03:38 AM.

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  5. #103
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    Quote Originally Posted by teepean47 View Post
    A small update: I uploaded BAM Analysis Kit to Github. PRs are welcome:

    github.com/teepean/BAM-Analysis-Kit
    If it is with PileUp Caller? Or what update it was?

  6. #104
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    Quote Originally Posted by teepean47 View Post
    I would like to keep them and I would like to know what is causing that.

    I had time to process the first one, PG2001.

    https://drive.google.com/open?id=1hv...Qg7KAyewO6XX3o
    Thanks.

    Actually, I really wanted this one though.

    https://www.ebi.ac.uk/ena/data/view/SAMEA5187658

  7. #105
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    Quote Originally Posted by sven.larson View Post
    If it is with PileUp Caller? Or what update it was?
    I haven't had the time to integrate pileupcaller yet as I cannot get it working properly.

  8. #106
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    Hey, could you also add some 23andme-format functionality, like converting the original 23andme file into vcf and splitting it into several vcf files by chromosome?
    Last edited by FenriR; 01-27-2019 at 09:16 PM.

  9. #107
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    Quote Originally Posted by FenriR View Post
    Hey, could you also add some 23andme-format functionality, like converting the original 23andme file into vcf and splitting it into several vcf files by chromosome?
    There's a Perl script for converting 23andme to vcf:

    https://github.com/arrogantrobot/23andme2vcf

    Or with bcftools and vcftools.

    https://samtools.github.io/bcftools/howtos/convert.html

    The last entry can be used to split vcf by chromosomes.

    https://www.biostars.org/p/173073/

    Code:
    #!/bin/bash
    
    ## Assumes uncompressed VCF, extracts entries by chromosomes using tabix and parallel:
    if [[ ${1: -4} != ".vcf" ]]
      then
      echo '[ERROR]: Please provide an uncompressed vcf file'
      exit; fi
    
    ## Get chromosomes that are present in the VCF:
    cat $1 | mawk '$1 ~ /^#/ {next} {print $1 | "sort -k1,1 -u"}' > ${1%.vcf}_chrs.txt
    
    ## Compress & index file with tabix:
    cat $1 | mawk '$1 ~ /^#/ {print $0;next} {print $0 | "sort -k1,1 -k2,2n"}' | bgzip -c > ${1%.vcf}_sorted.vcf.gz
    tabix -p vcf ${1%.vcf}_sorted.vcf.gz
    
    ## Extract files by chr:
    cat ${1%.vcf}_chrs.txt | parallel "tabix -h ${1%.vcf}_sorted.vcf.gz {} > ${1%.vcf}_{}.vcf"
    
    ## Usage: ./split_vcf_by_chr.sh input.vcf

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  11. #108
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    Quote Originally Posted by Generalissimo View Post
    Thanks.

    Actually, I really wanted this one though.

    https://www.ebi.ac.uk/ena/data/view/SAMEA5187658
    ENA ftp site has been extremely slow for a while and downloading this was an effort

    https://drive.google.com/open?id=10n...vNrSAOPztUr7Mx

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  13. #109
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    Quote Originally Posted by teepean47 View Post
    There's a Perl script for converting 23andme to vcf:

    https://github.com/arrogantrobot/23andme2vcf
    ...

    [/code]
    Thanks!

    another good option:
    https://github.com/genepi/23andme-tools

    ...
    git clone https://github.com/genepi/23andme-tools.git
    cd 23andme-tools
    mvn install
    java -jar vcf-tools-0.1.jar vcf-generator --in </path/to/genome> --ref </path/to/human_g1k_v37.fasta>
    --out <vcf-destination-folder> [--exclude <chromosomes to exclude>] [--split false]
    ...

  14. #110
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    Quote Originally Posted by FenriR View Post
    Thanks!

    another good option:
    If this is basically imputiation tool? 23me v5 converted to vcf and then uploaded to Gedmatch Genesis (there is such option for vcf), would have 160 000 snps instead of 55 000 in Gedmatch calcs or am I wrong?

    The VCF files are generated by combining information from your 23andMe data (.zip or .txt) with the human reference file. This project uses HTSJDK for many tasks.

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