Tagged with #exome sequencing
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Created 2013-10-15 09:02:45 | Updated | Tags:
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Dear GATK!

We are running an exome sequencing project where we have between 30 and 50 exomes in total. For optimal variant quality score recalibration we should use as much data as possible in the VariantRecalibrator step. However, for downstream analysis purposes, we want individual exome VCFs, and UnifiedGenotyper has been run individually for each sample. Our plan was to feed all data into VariantRecalibrator, and then run ApplyRecalibration on the individual raw VCFs. But VariantRecalibrator takes only one VCF as input, right? So what would be the best workflow for this scenario? Could we run UnifiedGenotyper to create a common VCF for Recalibration purposes only, and then apply this to the individual VCFs? Or would this somehow create an invalid input for the RECAL-file? Is it better to run variant calling and recalibration both on multi-sample VCFs and split the VCFs sample-wise later?


Lasse P

Created 2013-08-14 22:53:29 | Updated | Tags: snp
Comments (3)

I am running the Quality score recalibration and got an version error like this:

`java -Xmx4g -jar ~/GenomeAnalysisTK-2.1-3/GenomeAnalysisTK.jar -l INFO -R hg19.fa --DBSNP snp137.txt -I sdD1a_bam.marked.realigned.fixed.bam -T CountCovariates -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate -recalFile sdD1a.recal_data.csv & [11] 9980 [c@scigc-vm-10 shones]$ ##### ERROR ------------------------------------------------------------------------------------------

ERROR A USER ERROR has occurred (version 2.1-3-g8892c10):
ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
ERROR Please do not post this error to the GATK forum
ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR MESSAGE: Walker CountCovariates is no longer available in the GATK; it has been deprecated since version 2.0
ERROR ------------------------------------------------------------------------------------------`

Is there a solution for that? Thanks.

Created 2013-07-18 12:10:50 | Updated | Tags: pedigree
Comments (1)


Are there any GATK tools that can be used to check that samples in a pedigree are not mislabelled by looking for Mendelian inconsistencies in the exome sequencing data?