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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
    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

  6. #104
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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.

  7. #105
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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.

  8. #106
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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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  10. #107
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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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     Generalissimo (01-29-2019)

  12. #108
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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]
    ...

  13. #109
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    i am looking for fastest way of getting filtered autosomal raw data (Ftdna,23andme) from bam-file. If there is something better than B An. kit, can you please give me link where i can download and learn how to use it.

  14. #110
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    Quote Originally Posted by RasulSrg View Post
    i am looking for fastest way of getting filtered autosomal raw data (Ftdna,23andme) from bam-file. If there is something better than B An. kit, can you please give me link where i can download and learn how to use it.
    That would help

    https://github.com/tkrahn/extract23

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