Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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?

  • #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();

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Genetic Variation in Immunogenetics and Antibody Diversity
      by seqadmin



      The field of immunogenetics explores how genetic variations influence immune responses and susceptibility to disease. In a recent SEQanswers webinar, Oscar Rodriguez, Ph.D., Postdoctoral Researcher at the University of Louisville, and Ruben Martínez Barricarte, Ph.D., Assistant Professor of Medicine at Vanderbilt University, shared recent advancements in immunogenetics. This article discusses their research on genetic variation in antibody loci, antibody production processes,...
      Today, 07:24 PM
    • seqadmin
      Choosing Between NGS and qPCR
      by seqadmin



      Next-generation sequencing (NGS) and quantitative polymerase chain reaction (qPCR) are essential techniques for investigating the genome, transcriptome, and epigenome. In many cases, choosing the appropriate technique is straightforward, but in others, it can be more challenging to determine the most effective option. A simple distinction is that smaller, more focused projects are typically better suited for qPCR, while larger, more complex datasets benefit from NGS. However,...
      10-18-2024, 07:11 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, 11-01-2024, 06:09 AM
    0 responses
    24 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 10-30-2024, 05:31 AM
    0 responses
    21 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 10-24-2024, 06:58 AM
    0 responses
    25 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 10-23-2024, 08:43 AM
    0 responses
    55 views
    0 likes
    Last Post seqadmin  
    Working...
    X