Hello!

I'm trying to phase my genotypes based on the data for 8 trios of a sequenced organism using PhaseByTransmission, which fails with messages as listed below.

$ java -Xmx20g -jar ~/n/GenomeAnalysisTK-1.5-31-gadad76b/GenomeAnalysisTK.jar -R mygenome_sorted.fa -T PhaseByTransmission -V all_sorted_withHeader.vcf -ped Sample_info.ped -o all_phased_by_transmission.vcf 

INFO 20:54:02,919 HelpFormatter - Copyright (c) 2010 The Broad Institute 
INFO 20:54:02,920 HelpFormatter - Please view our documentation at <http://www.broadinstitute.org/gsa/wiki> 
INFO 20:54:02,920 HelpFormatter - For support, please view our support site at <http://getsatisfaction.com/gsa> 
INFO 20:54:02,920 HelpFormatter - Program Args: -R mygenome_sorted.fa -T PhaseByTransmission -V all_sorted_withHeader.vcf -ped Sample_info.ped -o all_phased_by_transmission.vcf 
INFO 20:54:02,921 HelpFormatter - Date/Time: 2012/04/22 20:54:02 
INFO 20:54:02,921 HelpFormatter - --------------------------------------------------------------------------------- 
INFO 20:54:02,921 HelpFormatter - --------------------------------------------------------------------------------- 
INFO 20:54:02,995 RodBindingArgumentTypeDescriptor - Dynamically determined type of all_sorted_withHeader.vcf to be VCF 
INFO 20:54:03,002 GenomeAnalysisEngine - Strictness is SILENT 
INFO 20:54:04,551 RMDTrackBuilder - Creating Tribble index in memory for file all_sorted_withHeader.vcf 
INFO 20:56:55,532 RMDTrackBuilder - Writing Tribble index to disk for file all_sorted_withHeader.vcf.idx 
INFO 20:57:00,377 PedReader - Reading PED file Sample_info.ped with missing fields: []
INFO 20:57:00,489 PedReader - Phenotype is other? false 
INFO 20:57:01,371 TraversalEngine - [INITIALIZATION COMPLETE; TRAVERSAL STARTING] 
INFO 20:57:01,371 TraversalEngine - Location processed.sites runtime per.1M.sites completed total.runtime remaining 
INFO 20:57:04,604 GATKRunReport - Uploaded run statistics report to AWS S3 
##### ERROR ------------------------------------------------------------------------------------------ 
##### ERROR stack trace 
java.lang.NumberFormatException: For input string: "." 
at java.lang.NumberFormatException.forInputString(NumberFormatException.java:48) 
at java.lang.Integer.parseInt(Integer.java:449) 
at java.lang.Integer.parseInt(Integer.java:499) 
at org.broadinstitute.sting.utils.variantcontext.GenotypeLikelihoods.parsePLsIntoLikelihoods(GenotypeLikelihoods.java:153) 
at org.broadinstitute.sting.utils.variantcontext.GenotypeLikelihoods.getAsVector(GenotypeLikelihoods.java:80) 
at org.broadinstitute.sting.utils.variantcontext.GenotypeLikelihoods.getAsMap(GenotypeLikelihoods.java:105) 
at org.broadinstitute.sting.gatk.walkers.phasing.PhaseByTransmission.getLikelihoodsAsMapSafeNull(PhaseByTransmission.java:519) 
at org.broadinstitute.sting.gatk.walkers.phasing.PhaseByTransmission.phaseTrioGenotypes(PhaseByTransmission.java:562) 
at org.broadinstitute.sting.gatk.walkers.phasing.PhaseByTransmission.map(PhaseByTransmission.java:762) 
at org.broadinstitute.sting.gatk.walkers.phasing.PhaseByTransmission.map(PhaseByTransmission.java:74) 
at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:78) 
at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:18) 
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:63) 
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:246) 
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:128) 
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236) 
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146) 
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:92) 
##### ERROR ------------------------------------------------------------------------------------------ 
##### ERROR A GATK RUNTIME ERROR has occurred (version 1.5-31-gadad76b): 
##### ERROR 
##### ERROR Please visit the wiki to see if this is a known problem 
##### ERROR If not, please post the error, with stack trace, to the GATK forum 
##### ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki 
##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa 
##### ERROR 
##### ERROR MESSAGE: For input string: "." 
##### ERROR ------------------------------------------------------------------------------------------

I suspect this is because of missing genotypes in lines like this (with dots corresponding to missing data):

#CHROM    POS    ID    REF    ALT    QUAL    FILTER    INFO    FORMAT    ERS074168    ERS074167 ERS074166    ERS074171    ERS074170    ERS074169 ERS074174    ERS074173 ERS074172    ERS074177    ERS074176    ERS074175    ERS074180    ERS074179 ERS074178    ERS074183    ERS074182 ERS074181    ERS074186    ERS074185 ERS074184    ERS074189    ERS074188    ERS074187 
1    160248    .    T    C    40.00    . AC1=6;AC=6;AF1=1;AN=6;DP4=0,0,3,0;DP=6;FQ=-28.1;MQ=29;SF=2;VDB=0.0046 GT:GQ:PL    .    .    .    . 1/1:3:0,0,0    1/1:3:0,0,0    1/1:10:72,9,0    .    .    .    .    .    .    .    .    .    .    .    .    .    .    .

Is there a different way I should format missing genotypes? Or has something else gone wrong?

Many thanks!