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  • binfoUser
    Member
    • Jan 2016
    • 22

    #1

    How to use .tbi for vcf file

    I want to use indexed vcf files. For that I have a file .vcf and another file .tbi
    I don't know how to use .tbi file. I'm using htsjdk library for Java but I don't know which methods to use.
    For what I searched I have to use TabixIndexCreator and BlockCompressedInputStream to index and to read the file. Can someone give any ideas how to do that?
  • binfoUser
    Member
    • Jan 2016
    • 22

    #2
    This is the code that I have so far:

    Code:
    VCFFileReader fileR= new VCFFileReader(f, fi, true);
    VCFHeader fileHeader = fileR.getFileHeader();
    VCFRecordCodec recCodec = new VCFRecordCodec(fileHeader);
            
    TabixIndexCreator tic = new TabixIndexCreator(TabixFormat.VCF);
            
    BlockCompressedInputStream inputStream = new BlockCompressedInputStream(new File("ex.vcf.gz")); 
    long p = 0;
    String rrline = inputStream.readLine();
    
    CloseableIterator<VariantContext> vc = fileR.iterator();
        while(vc.hasNext()){
             VariantContext v = vc.next();
              tic.addFeature(v, p);
              p = inputStream.getFilePointer();
              rrline = inputStream.readLine();

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