Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • VCF NC Format

    Hi,

    I ran VARSCAN2 mpileup2snp to call SNPs and generated a vcf file.

    However, I noticed a strange thing about the NC flag. This is apparently INFO=<id=nc,number=1,type=integer,description="number of="" samples="" not="" called"="">

    However, I see

    Code:
    TR43100|c0_g1_i1    792 .   T   C   .   PASS    ADP=0;WT=1;HET=0;HOM=1;NC=17    GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR    ./.:.:0 ./.:.:0 ./.:.:0 ./.:.:1 ./.:.:0 ./.:.:1 ./.:.:0 ./.:.:0 ./.:.:1 0/0:10:5:5:5:0:0%:1E0:38:0:0:5:0:0  ./.:.:0 ./.:.:1 ./.:.:1 1/1:7:2:2:0:2:100%:1.6667E-1:0:33:0:0:1:1   ./:.:0  ./:.:0  ./:.:0  ./:.:0  ./:.:0
    This has NC=17 and I can see from the 19 samples 2 have been called. This seems correct.

    Code:
    TR43100|c1_g1_i1    351 .   T   C   .   PASS    ADP=0;WT=1;HET=1;HOM=0;NC=17    GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR    ./:.:0  ./:.:0  ./:.:0  ./:.:0  ./:.:0  ./:.:1  ./:.:0  ./:.:0  ./:.:0  ./:.:2  ./:.:0  ./:.:0  ./:.:0  0/1:6:4:4:2:2:50%:2.1429E-1:40:38:2:0:1:1   ./:.:0  ./:.:0  ./:.:0  ./:.:0  ./:.:0
    This has NC=17 abut I can only see one sample that has been called? What have I missed, why isn't NC=18 here?

    And it says WT=1. Where is the WT? This should be 0/0

    And also
    Code:
    TR43100|c0_g1_i1 763 . G A . PASS ADP=0;WT=2;HET=0;HOM=1;NC=16 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR ./.:.:0 ./.:.:0 ./.:.:0 1/1:13:3:3:0:3:100%:5E-2:0:39:0:0:0:3 ./.:.:0 ./.:.:1 ./.:.:0 ./.:.:0 ./.:.:1 0/0:6:3:3:3:0:0%:1E0:40:0:0:3:0:0 ./.:.:0 ./.:.:1 ./.:.:1 ./.:.:2 ./.:.:0 ./.:.:0 ./.:.:0 ./.:.:0 ./.:.:0
    Where are the 2 WT? I can only see 1 0/0
    Last edited by GenoMax; 03-07-2016, 08:12 AM. Reason: added CODE tags to improve readability

  • #2
    For reference/cross-posted: https://www.biostars.org/p/180308/

    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,...
      11-06-2024, 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, 11-08-2024, 11:09 AM
    0 responses
    226 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 11-08-2024, 06:13 AM
    0 responses
    166 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 11-01-2024, 06:09 AM
    0 responses
    80 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 10-30-2024, 05:31 AM
    0 responses
    27 views
    0 likes
    Last Post seqadmin  
    Working...
    X