Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • angieant
    started a topic Help: error while running VariantRecalibrator

    Help: error while running VariantRecalibrator

    experiment: target enrichment and sequencing using Illumina platform

    raw VCF file from UnifiedGenotyper -> Variantrecalibrator

    i got the following error, any potential explanation? Thanks

    "
    ##### ERROR MESSAGE: Bad input: Error during negative model training. Minimum number of variants to use in training is larger than the whole call set. One can attempt to lower the --minNumBadV ariants arugment but this is unsafe.
    "

    script used:

    java -Xmx4g -jar GenomeAnalysisTK.jar -T VariantRecalibrator -T \
    -mode BOTH -nt 4 \
    -R hg19_all_MT.fasta \
    -input two.final.vcf \
    -resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.b37.sites.fy_left.vcf \
    -resourcemni,known=false,training=true,truth=false,prior=12.0 1000G_omni2.5.b37.site.fy.vcf \
    -resource:dbsnp,known=true,training=false,truth=false,prior=8.0 dbsnp137_sort_fy_left.vcf \
    -recalFile two.final.vcf.reca \
    -tranchesFile two.final.vcf.tranches \
    -rscriptFile two.final.vcf.R \
    -tranche 100.0 -tranche 99.9 -tranche 99.0 -tranche 90.0 -tranche 85.0 -tranche 80.0 \
    -an QD -an HaplotypeScore -an MQRankSum -an ReadPosRankSum -an MQ -an FS -an HRun

Latest Articles

Collapse

  • seqadmin
    Recent Advances in Sequencing Technologies
    by seqadmin







    Innovations in next-generation sequencing technologies and techniques are driving more precise and comprehensive exploration of complex biological systems. Current advancements include improved accessibility for long-read sequencing and significant progress in single-cell and 3D genomics. This article explores some of the most impactful developments in the field over the past year.

    Long-Read Sequencing
    Long-read sequencing has...
    12-02-2024, 01:49 PM
  • 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

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 12-02-2024, 09:29 AM
0 responses
149 views
0 likes
Last Post seqadmin  
Started by seqadmin, 12-02-2024, 09:06 AM
0 responses
51 views
0 likes
Last Post seqadmin  
Started by seqadmin, 12-02-2024, 08:03 AM
0 responses
42 views
0 likes
Last Post seqadmin  
Started by seqadmin, 11-22-2024, 07:36 AM
0 responses
74 views
0 likes
Last Post seqadmin  
Working...
X