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  • werno
    replied
    Heterozygous filtering

    Hello everybody,

    can you help me how to filter heterozygous variants in vcf file?

    thank in advance for answer

    with best regards

    werno

    Leave a comment:


  • Seqql
    replied
    Good thought, it worked.
    Thanks for the help

    Leave a comment:


  • lindenb
    replied
    11,30 is generated by my program (?) If yes, this is a locale problem:
    try to set the LANG variable


    $ export LANG=en_US.UTF-8
    $ echo $LANG
    en_US.UTF-8




    or/and (?) specify it on the command line:

    java -Duser.language=en -Duser.country=US (...)
    Last edited by lindenb; 06-03-2015, 08:16 AM.

    Leave a comment:


  • Seqql
    replied
    Thank you, this is looknig very promising.

    I got the filtered vcf file, but i've run into a problem.
    I can't load the file into IGV because of the FILTER field, values like "11,30" aren't accepted. Looks like IGV only accepts one number with/out dots ("11.30" is ok).

    Is there any quick fix for this I could apply to the code? If not i may just delete the whole column.

    Leave a comment:


  • lindenb
    replied
    --keep-filtered is for the FILTER column

    to answer this, I would use my tool https://github.com/lindenb/jvarkit/wiki/VCFFilterJS


    java -jar dist/vcffilterjs.jar -e 'variant.getGenotype(0).isHomVar()' file.vcf

    Leave a comment:


  • Filtering homozygous variants in vcf file with vcftools

    Hi everybody,

    I'm trying to modify a vcf file to keep only homozygous variants.
    I've tried using vcftools, but i can't get the syntax right.

    I thought using the "keep-filtered" option of vcftools should be the right approach. Also I'm trying to find homozygous variants by the "GT 1/1" tag.

    I've tried
    vcftools --keep-filtered GT:1/1 --vcf in.vcf --out out.vcf
    but it kept none.

    edit:
    vcf file looks like this:
    c130956_g1_i1 50 . A C 5.49 . DP=2;RPB=-9.668049e-01;AF1=0.5049;AC1=1;DP4=1,0,1,0;MQ=33;FQ=-10.5;PV4=1,1,1,1 GT:PL: DP:GQ 0/1:34,0,17:2:22
    c130956_g1_i1 62 . T A 49 . DP=3;VDB=5.867524e-02;AF1=1;AC1=2;DP4=0,0,2,1;MQ=30;FQ=-36 GT:PL: DP:GQ 1/1:81,9,0:3:16




    What is the right syntax here?
    Last edited by Seqql; 06-03-2015, 06:08 AM.

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