Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Variants called using GATK from samples of Nextera and TruSeq exome enrichment kits

    I am doing variant calling for exomes generated from Illumina HiSeq 2000, with Nextera Exome Enrichment kit.
    Earlier I used the same variant calling pipeline to call variants from sequences based on TruSeq Exome Enrichment kit.
    Now with the Nextera Exome Enrichment kit, I find that the number of variants called using GATK is reduced to almost half as compared to TruSeq.
    I am not able to reach a conclusion as to why this drastic reduction in number.

    TruSeq sample Nextera sample
    Mean coverage 40X 47.5X
    GATK variants 53917 27596

    Here is the GATK command I used for calling variants for both TruSeq and Nextera samples:
    java -Xmx2g -Djava.io.tmpdir=temp -jar $gatk_jar -T UnifiedGenotyper -I $in -R $ucsc_hg19_fasta -D:name,VCF $dbsnp146_hg19_vcf -o $o -dcov 1000 -A AlleleBalance -A BaseCounts -A VariantType -baq CALCULATE_AS_NECESSARY -stand_call_conf 30.0 -stand_emit_conf 10.0 -glm BOTH -L $nextera_target_bed(or $truseq_target_bed )

  • #2
    A few possible explanations:

    1) higher error rate in the sequence data from the TruSeq sample, producing false-positive variant calls. You can use FastQC to assess the base quality metrics of the two data sets.

    2) capture of highly polymorphic loci in the TruSeq but not Nextera enrichment. Compare the covered intervals with Bedtools, and see if there's a large difference in variant frequency between the shared vs unique regions.

    Comment

    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, Yesterday, 06:37 PM
    0 responses
    8 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, Yesterday, 06:07 PM
    0 responses
    8 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-22-2024, 10:03 AM
    0 responses
    49 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-21-2024, 07:32 AM
    0 responses
    67 views
    0 likes
    Last Post seqadmin  
    Working...
    X