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Weird VariantRecalibration result, should i add exome data from 1000G project into WES analysis?

wlaiwlai Member
edited February 27 in Ask the GATK team
Hi, attached below is the result of running VariantRecalibration on the chr1 of 56 individuals? Seems like there is no true positive discovered when truth sensitivity is 100.

known=(602444 @ 1.6475) novel=(238870 @ 0.3388)

gatk VariantRecalibrator -R $reference
-V ./LB56sa_chr1_output.vcf.gz
--resource hapmap,known=false,training=true,truth=true,prior=15.0:$hapmap
--resource omni,known=false,training=true,truth=false,prior=12.0:$omni
--resource 1000G,known=false,training=true,truth=false,prior=10.0:$oneKsnp
--resource dbsnp,known=true,training=false,truth=false,prior=2.0:$dbsnp
-an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR -mode SNP
-O LB56_chr1.output.recal
--tranches-file LB56_chr1.tranches
--rscript-file LB56.plots.R

May i have any advice on this case?
Post edited by wlai on

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  • wlaiwlai Member
    edited March 22
    thank you bhanum
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