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# PhasebyTransmission error concerning Genotype Likelihood score

Posts: 5Member
edited June 2013

Hello Team,

I am attempting to run GATK's PhasebyTransmission command to phase a vcf file contains a father, mother, son trio generated from complete genomics mkvcf command.

After creating the ped file and running the command I generate the error: "MESSAGE: BUG: Attempted to get likelihoods as strings and neither the vector nor the string is set!". I am not exactly sure what this means.

When I check my file and the documentation I am able to see that the 'GL' field is contained in the file, but could this not be the case? I have attached a few lines from the vcf I am using.

Any help with resolving the this issue would be of great help.

Thank you

JumaQuar

Post edited by JumaQuar on
Tagged:

Hi there,

Can you please tell me what version of GATK you are using? Also, have you validated your VCF file?

Geraldine Van der Auwera, PhD

• Posts: 5Member

GATK version: version 2.5-2-gf57256b

I identified a few formatting errors from the CGI tools output that I corrected which allowed ValidateVariants to fully complete. When I tried to run the the phasebytransmission command I get this error:

##### ERROR stack trace

java.lang.ArrayIndexOutOfBoundsException: 1 at org.broadinstitute.variant.variantcontext.GenotypeLikelihoods.getAsMap(GenotypeLikelihoods.java:163) at org.broadinstitute.sting.gatk.walkers.phasing.PhaseByTransmission.getLikelihoodsAsMapSafeNull(PhaseByTransmission.java:601) at org.broadinstitute.sting.gatk.walkers.phasing.PhaseByTransmission.phaseTrioGenotypes(PhaseByTransmission.java:644) at org.broadinstitute.sting.gatk.walkers.phasing.PhaseByTransmission.map(PhaseByTransmission.java:849) at org.broadinstitute.sting.gatk.walkers.phasing.PhaseByTransmission.map(PhaseByTransmission.java:127) at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:268) at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:256) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245) at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:145) at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92) at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:100) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:286) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:245) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)

##### ERROR ------------------------------------------------------------------------------------------

I have attached my updated vcf file, any help would be greatly appreciated.

• Posts: 5Member
edited June 2013

Also, here are the command and .ped file I am using.

ped file:

Family_63   GS000009556-ASM 0   0   1   2
Family_63   GS000009551-ASM 0   0   2   1
Family_63   GS000008961-ASM GS000009556-ASM GS000009551-ASM 1   2


Command:

java -Xmx1g -jar /home/dquarless/bin/GenomeAnalysisTK-2.5-2-gf57256b/GenomeAnalysisTK.jar -R /projects/stsi/data/GRCh37/GRCh37_p2/BWA_index/GRCh37.chr1_22_XYMT.fa -T PhaseByTransmission -V input.vcf -ped Family_63.ped -o Family_63_output.vcf

Post edited by Geraldine_VdAuwera on

OK, we'll have a look at this and try to debug it locally. I'll let you know what we find.

Geraldine Van der Auwera, PhD

FYI there are three line breaks in the vcf file you posted that shouldn't be there (lines 61-62, 71-72, 77-78). That's not the cause of your issue but next time please make sure that the data you give us is in good shape, otherwise it needlessly increases the time we spend debugging your issue...

Geraldine Van der Auwera, PhD

• Posts: 5Member

This answer was amazing! Thank you for the help. Catching the validation pass would have been tricky.

Best!