Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • How to write in VCF file for a deletion that occurs at position 1?

    If a deletion happens at position 2, (like T below), in VCF, it is writen:

    POS REF ALT
    1 AT A

    what if at position 1, A is deleted, how to record it in VCF?
    Thanks!

    Jeff

  • #2
    any clue? who can I refer this to?

    Comment


    • #3
      Well, looking at the 1000genomes page on VCF they say [emphasis mine]:

      REF reference base(s): Each base must be one of A,C,G,T,N (case insensitive). Multiple bases are permitted. The value in the POS field refers to the position of the first base in the String. For simple insertions and deletions in which either the REF or one of the ALT alleles would otherwise be null/empty, the REF and ALT Strings must include the base before the event (which must be reflected in the POS field), unless the event occurs at position 1 on the contig in which case it must include the base after the event; this padding base is not required (although it is permitted) for e.g. complex substitutions or other events where all alleles have at least one base represented in their Strings. If any of the ALT alleles is a symbolic allele (an angle-bracketed ID String "<ID>") then the padding base is required and POS denotes the coordinate of the base preceding the polymorphism. Tools processing VCF files are not required to preserve case in the allele Strings. (String, Required).

      Comment


      • #4
        Thanks!

        Does this mean if A at (poistion 1) is deleted, it should be recorded as

        POS REF ALT
        1 AT T

        ?

        Comment

        Latest Articles

        Collapse

        • seqadmin
          Best Practices for Single-Cell Sequencing Analysis
          by seqadmin



          While isolating and preparing single cells for sequencing was historically the bottleneck, recent technological advancements have shifted the challenge to data analysis. This highlights the rapidly evolving nature of single-cell sequencing. The inherent complexity of single-cell analysis has intensified with the surge in data volume and the incorporation of diverse and more complex datasets. This article explores the challenges in analysis, examines common pitfalls, offers...
          06-06-2024, 07:15 AM
        • seqadmin
          Latest Developments in Precision Medicine
          by seqadmin



          Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

          Somatic Genomics
          “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
          05-24-2024, 01:16 PM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, Today, 07:49 AM
        0 responses
        12 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, Yesterday, 07:23 AM
        0 responses
        14 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 06-17-2024, 06:54 AM
        0 responses
        16 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 06-14-2024, 07:24 AM
        0 responses
        24 views
        0 likes
        Last Post seqadmin  
        Working...
        X