Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Samtools VCF file: NS field value missing/not printing

    Hi,

    In my VCF files, the NS field (Number of Samples With Data) is entirely missing. I would like to get this number so I can filter SNPs based on % of individuals with missing data.

    I am using mpileup on 100 individuals of a population, followed by bcf to vcf conversion.

    $ samtools-0.1.19/samtools mpileup -B -uD -Q 20 -f reference.fa Ind1.sorted.bam Ind2.sorted.bam [...] Ind100.sorted.bam | bcftools view -bvcg - > SNP.bcf

    followed by

    $ samtools-0.1.19/bcftools/bcftools view SNP.bcf | vcfutils.pl varFilter -D 5000 > SNP.vcf

    The vcf file version is 4.1

    Any help would be greatly appreciated. Thanks.

    Edit: This is what I get under 'INFO' column:
    DP=143;QS=0.897417,0.102583,0.000000,0.000000;VDB=6.988258e-06;RPB=5.927889e+00;AF1=0.09297;AC1=26;DP4=2,127,0,13;MQ=29;FQ=999;PV4=1,0.0071,1,1
    Last edited by probean; 02-07-2014, 02:07 PM.

Latest Articles

Collapse

  • seqadmin
    Strategies for Sequencing Challenging Samples
    by seqadmin


    Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
    03-22-2024, 06:39 AM
  • seqadmin
    Techniques and Challenges in Conservation Genomics
    by seqadmin



    The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

    Avian Conservation
    Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
    03-08-2024, 10:41 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 03-27-2024, 06:37 PM
0 responses
12 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-27-2024, 06:07 PM
0 responses
11 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-22-2024, 10:03 AM
0 responses
53 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-21-2024, 07:32 AM
0 responses
68 views
0 likes
Last Post seqadmin  
Working...
X