I have been trying tu run the VariantRecalibrator on my vcf with the standard command line suggested here:
https://gatkforums.broadinstitute.org/gatk/discussion/2805/howto-recalibrate-variant-quality-scores-run-vqsr
Command line I used is this:
gatk -T VariantRecalibrator \
-R /Users/debortoli/Doutorado/hg19/hg19.fa \
-input test_raw_snps.vcf \
-resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.hg19.sites.vcf \
-resource:omni,known=false,training=true,truth=true,prior=12.0 1000G_omni2.5.hg19.sites.vcf \
-resource:1000G,known=false,training=true,truth=false,prior=10.0 1000G_phase1.snps.high_confidence.hg19.sites.vcf \
-resource:dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_138.hg19.vcf \
-an QD \
-an FS \
-an SOR \
-an MQ \
-an MQRankSum \
-an ReadPosRankSum \
-an InbreedingCoeff \
-mode SNP \
-tranche 100.0 \
-tranche 99.9 \
-tranche 99.0 \
-tranche 90.0 \
-recalFile recalibrate_SNP.recal \
-tranchesFile recalibrate_SNP.tranches \
-rscriptFile recalibrate_SNP_plots.R
After some minutes running I get this error:
INFO 18:54:29,091 HelpFormatter - The Genome Analysis Toolkit (GATK) vexported, Compiled 2017/07/31 02:32:19
INFO 18:54:29,091 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
INFO 18:54:29,091 HelpFormatter - For support and documentation go to https://www.broadinstitute.org/gatk
INFO 18:54:29,091 HelpFormatter - [Thu Dec 07 18:54:29 BRST 2017] Executing on Mac OS X 10.13.1 x86_64
INFO 18:54:29,092 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_141-b15 JdkDeflater
INFO 18:54:29,095 HelpFormatter - Program Args: -T VariantRecalibrator -R /Users/debortoli/Doutorado/hg19/hg19.fa -input oca2_herc2_raw_snps.vcf -resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.hg19.sites.vcf -resource:omni,known=false,training=true,truth=true,prior=12.0 1000G_omni2.5.hg19.sites.vcf -resource:1000G,known=false,training=true,truth=false,prior=10.0 1000G_phase1.snps.high_confidence.hg19.sites.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_138.hg19.vcf -an QD -an FS -an SOR -an MQ -an MQRankSum -an ReadPosRankSum -an InbreedingCoeff -mode SNP -tranche 100.0 -tranche 99.9 -tranche 99.0 -tranche 90.0 -recalFile recalibrate_SNP.recal -tranchesFile recalibrate_SNP.tranches -rscriptFile recalibrate_SNP_plots.R
INFO 18:54:29,108 HelpFormatter - Executing as debortoli@MacBook-Pro on Mac OS X 10.13.1 x86_64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_141-b15.
INFO 18:54:29,108 HelpFormatter - Date/Time: 2017/12/07 18:54:29
INFO 18:54:29,109 HelpFormatter - --------------------------------------------------------------------------
INFO 18:54:29,109 HelpFormatter - --------------------------------------------------------------------------
INFO 18:54:29,132 GenomeAnalysisEngine - Strictness is SILENT
INFO 18:54:29,234 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 18:54:29,832 GenomeAnalysisEngine - Preparing for traversal
INFO 18:54:29,837 GenomeAnalysisEngine - Done preparing for traversal
INFO 18:54:29,837 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 18:54:29,837 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 18:54:29,838 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
INFO 18:54:29,842 TrainingSet - Found hapmap track: Known = false Training = true Truth = true Prior = Q15.0
INFO 18:54:29,842 TrainingSet - Found omni track: Known = false Training = true Truth = true Prior = Q12.0
INFO 18:54:29,843 TrainingSet - Found 1000G track: Known = false Training = true Truth = false Prior = Q10.0
INFO 18:54:29,843 TrainingSet - Found dbsnp track: Known = true Training = false Truth = false Prior = Q2.0
INFO 18:54:59,845 ProgressMeter - chr1:180418989 3596240.0 30.0 s 8.0 s 5.8% 8.6 m 8.1 m
INFO 18:55:29,853 ProgressMeter - chr2:89269200 7377132.0 60.0 s 8.0 s 10.9% 9.1 m 8.1 m
INFO 18:55:59,866 ProgressMeter - chr3:27451056 1.1488123E7 90.0 s 7.0 s 16.8% 8.9 m 7.4 m
INFO 18:56:29,873 ProgressMeter - chr4:6767822 1.5567576E7 120.0 s 7.0 s 22.5% 8.9 m 6.9 m
INFO 18:56:59,879 ProgressMeter - chr4:180178303 1.9568326E7 2.5 m 7.0 s 28.1% 8.9 m 6.4 m
INFO 18:57:29,882 ProgressMeter - chr6:13510279 2.439402E7 3.0 m 7.0 s 34.8% 8.6 m 5.6 m
INFO 18:57:59,894 ProgressMeter - chr7:7711400 2.8355875E7 3.5 m 7.0 s 40.1% 8.7 m 5.2 m
INFO 18:58:29,905 ProgressMeter - chr8:12472026 3.2353219E7 4.0 m 7.0 s 45.4% 8.8 m 4.8 m
INFO 18:58:59,918 ProgressMeter - chr9:29350711 3.6268024E7 4.5 m 7.0 s 50.7% 8.9 m 4.4 m
INFO 18:59:29,930 ProgressMeter - chr10:82904883 4.0231189E7 5.0 m 7.0 s 57.0% 8.8 m 3.8 m
ERROR --
ERROR stack trace
java.lang.ArrayIndexOutOfBoundsException: -32
at org.broadinstitute.gatk.utils.BaseUtils.convertIUPACtoN(BaseUtils.java:215)
at org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.java:347)
at org.broadinstitute.gatk.engine.datasources.providers.LocusReferenceView.initializeReferenceSequence(LocusReferenceView.java:163)
at org.broadinstitute.gatk.engine.datasources.providers.LocusReferenceView.(LocusReferenceView.java:139)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:90)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:311)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:113)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:255)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:157)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)
ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version exported):
ERROR
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, with stack trace, to the GATK forum.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions https://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: -32
ERROR ------------------------------------------------------------------------------------------
Any thoughts about what can I do in this case?
Thanks