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Old 08-28-2020, 07:27 AM   #1
Oscar_Alonso_Luna
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Location: Mexico City

Join Date: Jan 2019
Posts: 1
Question 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 at 08:21 AM. Reason: Added [CODE] tags
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