I was wondering if anyone has used VQSR for a mouse related genome project. I am working with mm10 dbsnp and DNA-seq short insert data for multiple homozygous mouse samples. I have obtained decent results so far using the mm10 dbsnp as the training set, but was curious to see if anyone had any recommendations as to what settings to use. Any input is appreciated. I also have a lot of RNA-seq data, but that will come at a much later point in time. Thanks!
Dear all,
I was calling SNP from Mouse samples using GATK and was in the step of "Variant quality score recalibration". The VariantRecalibrator walker asked me to provide training sets for mouse SNPs. The only SNP data (for the USCS mm9 assembly) I can find right now is the dbSNP. So I tried the run VariantRecalibrator like this:
java -Xmx4g -jar GenomeAnalysisTK.jar -T VariantRecalibrator -R Refseq.fa -input snps.raw.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=6.0 snp128.vcf -an QD -an HaplotypeScore -an MQRankSum -an ReadPosRankSum -an FS -an MQ -an InbreedingCoeff -mode BOTH -recalFile output.recal -tranchesFile output.tranches -rscriptFile output.plots.R
However, the program asked for more:
I was wondering if I can change the parameters by setting both the training/truth to true:
-resource:dbsnp,known=true,training=true,truth=true,prior=6.0 snp128.vcf
or should I ignore the "-resource" option at the cost of being less accurate?
Any suggestions would be greatly appreciated.
Thanks!
Tuo
Hello, I am just trying VariantRecalibrator on my 4 samples:
java -jar GenomeAnalysisTK.jar -T VariantRecalibrator -R gatk.ucsc.mm10.fa -input UnifiedGenotyper.output.snps.raw.vcf -nt 14 -recalFile file_for_ApplyRecalibration.recal -tranchesFile file_for_ApplyRecalibration.tranches -resource:sanger,known=false,training=true,truth=true mgp.v2.snps.annot.reformat.vcf -resource:dbnsp,known=true,training=false,truth=false,prior=6.0 mm10_dbsnp.vcf -an QD -an HaplotypeScore -an MQRankSum -an ReadPosRankSum -an FS -an MQ -an InbreedingCoeff -mG 4 -percentBad 0.05
which starts running then gives me this error: INFO 08:26:57,741 GATKRunReport - Uploaded run statistics report to AWS S3
java.lang.NumberFormatException: For input string: "." at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65) at java.lang.Integer.parseInt(Integer.java:481) at java.lang.Integer.valueOf(Integer.java:582) at org.broadinstitute.sting.utils.codecs.vcf.AbstractVCFCodec.decodeInts(AbstractVCFCodec.java:680) at org.broadinstitute.sting.utils.codecs.vcf.AbstractVCFCodec.createGenotypeMap(AbstractVCFCodec.java:641) at org.broadinstitute.sting.utils.codecs.vcf.AbstractVCFCodec$LazyVCFGenotypesParser.parse(AbstractVCFCodec.java:92) at org.broadinstitute.sting.utils.variantcontext.LazyGenotypesContext.decode(LazyGenotypesContext.java:130) at org.broadinstitute.sting.utils.variantcontext.LazyGenotypesContext.getGenotypes(LazyGenotypesContext.java:120) at org.broadinstitute.sting.utils.variantcontext.GenotypesContext.iterator(GenotypesContext.java:461) at org.broadinstitute.sting.utils.variantcontext.VariantContext.getCalledChrCount(VariantContext.java:922) at org.broadinstitute.sting.utils.variantcontext.VariantContext.getCalledChrCount(VariantContext.java:908) at org.broadinstitute.sting.utils.variantcontext.VariantContext.isMonomorphicInSamples(VariantContext.java:937) at org.broadinstitute.sting.utils.variantcontext.VariantContext.isPolymorphicInSamples(VariantContext.java:948) at org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantDataManager.isValidVariant(VariantDataManager.java:278) at org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantDataManager.parseTrainingSets(VariantDataManager.java:263) at org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator.map(VariantRecalibrator.java:259) at org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator.map(VariantRecalibrator.java:107) at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:243) at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:231) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:248) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:219) at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:120) at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:67) at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:23) at org.broadinstitute.sting.gatk.executive.ShardTraverser.call(ShardTraverser.java:73) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334) at java.util.concurrent.FutureTask.run(FutureTask.java:166) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) at java.lang.Thread.run(Thread.java:722)
I've used all three VCFs in other GATK tools without issues. Any help greatly appreciated!, many thanks, Lavinia.
