Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • VQSR mixture model and tranches plot doubts (GATK 4.1.7.0)

    Hello everyone:

    I am processing 74 germline exome sequencing samples of Mexican childhood patients on GATK 4.1.7.0. After VariantRecalibrator SNP, 2D projection of Gaussian mixture model does not show clearly high quality cluster of SNPs (green area), therefore, tranches plot does not show TPs variantes and Ti/Tv < 2.0
    (attached below as plots.pdf)


    The 74 BAM included in joint Genotyping approach, have a 60 - 85% of bases 20X. The script used and resource data sets are the following:
    Code:
    GATK VariantRecalibrator -R Homo_sapiens_assembly19.fasta -V input.vcf --resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.b37.vcf --resource:omni,known=false,training=true,truth=false,prior=12.0 1000G_omni2.5.b37.vcf --resource:1000G,known=false,training=true,truth=false,prior=10.0 1000G_phase1.snps.high_confidence.b37.vcf --resource:dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_138.b37.vcf -an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR -mode SNP -O output.recal --tranches-file Px_piloto.tranches --rscript-file file.plots.R
    What does it mean? Have you any suggestions?
    Last edited by GenoMax; 08-28-2020, 07:21 AM. Reason: Added [CODE] tags

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
11 views
0 likes
Last Post seqadmin  
Started by seqadmin, Yesterday, 06:07 PM
0 responses
10 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-22-2024, 10:03 AM
0 responses
51 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