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Old 09-10-2011, 08:58 PM   #1
Location: shanghai

Join Date: Nov 2010
Posts: 24
Default problem about GATK indel VQSR

java -Xmx4g -jar GenomeAnalysisTK-1.1-36-g367bbee/GenomeAnalysisTK.jar \
-T VariantRecalibrator \
-R ucsc.hg19.fasta \
-B:input,VCF s1_raw_indel.vcf \
-B:training,VCF,known=true,training=true,truth=true,prior=12.0 indels_mills_devine.hg19.sites.vcf \
-an QD -an FS -an HaplotypeScore -an ReadPosRankSum \
-mode INDEL \
-recalFile s1_raw_indel.recal \
-tranchesFile s1_raw_indel.tranches \
-rscriptFile s1_raw_indel_plots.R

when I run this GATK command followed :
Indel specific recommendations

We use the (Mills, Devine, Genome Research, 2011) dataset as training data when modeling indels with the VQSR. This dataset is available in the GATK resource bundle.
Arguments for VariantReacalibrator:
-B:training,VCF,known=true,training=true,truth=true,prior=12.0 indels_mills_devine.b37.sites.vcf \
-an QD -an FS -an HaplotypeScore -an ReadPosRankSum -an InbreedingCoeff \
-mode INDEL \

I got this error:
##### ERROR MESSAGE: NaN LOD value assigned. Clustering with this few variants and these annotations is unsafe.

please help me,and the snp VariantRecalibrator is all right.
wanguan2000 is offline   Reply With Quote
Old 09-10-2011, 11:27 PM   #2
Location: shanghai

Join Date: Nov 2010
Posts: 24

ps: s1_raw_indel.vcf file contains total of 8454 indels, are the number is few variants and these annotations is unsafe?
wanguan2000 is offline   Reply With Quote
Old 11-07-2011, 06:15 AM   #3
Location: Iowa City, IA

Join Date: Jun 2011
Posts: 24

Gaussian modeling might not be appropriate for indels. I did manual filtering following a pipeline for exome sequence posted here.
liu_xt005 is offline   Reply With Quote

gatk, indel, vqsr

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