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 : http://www.broadinstitute.org/gsa/wi...th_the_GATK_v3
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.
-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 : http://www.broadinstitute.org/gsa/wi...th_the_GATK_v3
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.
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