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Created 2016-04-08 06:46:30 | Updated | Tags: vqsr plots

Comments (1)

Hi,

I ran VQSR with 150+ whole genome samples. Attached is one of the Gaussian mixture model plots. I have read the VQSR guide on how to interpret the plots but I am not quite understand. Referring to the plot, green area represents good quality variants while variants fall in red area should be filtered out, the annotations MQ and QD are plotted against each other. For MQ, i can see that good quality variants have MQ around 60. What about QD? What can I do with these plots?

JF


Created 2015-04-24 08:31:06 | Updated | Tags: baserecalibrator plots

Comments (2)

Hi,

I am using the latest version of GATK. But it is giving me the below error, though i have specified the argument

-o $DATPATH/recal.grp \ -plots $DATPATH/recal.grp.pdf

ERROR ------------------------------------------------------------------------------------------ ERROR A USER ERROR has occurred (version 3.3-0-g37228af): ERROR MESSAGE: Argument with name 'plots' isn't defined. ERROR ------------------------------------------------------------------------------------------ Please advise on this.

Thanks


Created 2013-09-17 09:58:33 | Updated 2013-09-17 10:38:55 | Tags: variantrecalibrator plots

Comments (1)

Hi,

I am running the INDEL model of VariantRecalibrator with GATK 1.6 (last license-compatible version in our hands), and the very last step seems to crash when writing the plot using plot_Tranches.R (see below).

All the previous steps seem to run well on 9G RAM and I presume this plotting step just produces an image to manually inspect and nothing else. Is it possible to switch off the plotting step at all?

Thanks

java -Xmx8g -jar /my/path/GATK/GenomeAnalysisTK.jar -et NO_ET -T VariantRecalibrator -R /my/path/WholeGenomeFASTA/genome.fa -input /my/path/genome.vcf.tmp2 -resource:mills,known=true,training=true,truth=true,prior=12.0 /my/path/Annotation/Mills_Devine_2hit.indels.hg19.vcf -an QD -an FS -an ReadPosRankSum -an DP --mode INDEL -recalFile /my/path/test/file.INDEL.recal -tranchesFile /my/path/test/file.INDEL.tranches

[...] INFO 10:46:37,310 VariantRecalibrator - Writing out recalibration table... INFO 10:46:46,202 VariantRecalibrator - Executing: Rscript (resource)org/broadinstitute/sting/gatk/walkers/variantrecalibration/plot_Tranches.R /my/path/test/file.INDEL.tranches 2.15

PS: I tried adding the option "-rscriptFile /dev/null", but it also seems to crash at the same step: INFO 11:25:10,870 VariantRecalibrator - Executing: Rscript /dev/null