The current GATK version is 3.7-0
Examples: Monday, today, last week, Mar 26, 3/26/04

#### Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

You can opt in to receive email notifications, for example when your questions get answered or when there are new announcements, by following the instructions given here.

#### ☞ Got a problem?

1. Search using the upper-right search box, e.g. using the error message.
3. Include tool and Java versions.
4. Tell us whether you are following GATK Best Practices.
5. Include relevant details, e.g. platform, DNA- or RNA-Seq, WES (+capture kit) or WGS (PCR-free or PCR+), paired- or single-end, read length, expected average coverage, somatic data, etc.
6. For tool errors, include the error stacktrace as well as the exact command.
7. For format issues, include the result of running ValidateSamFile for BAMs or ValidateVariants for VCFs.
8. For weird results, include an illustrative example, e.g. attach IGV screenshots according to Article#5484.
9. For a seeming variant that is uncalled, include results of following Article#1235.

#### ☞ Formatting tip!

Wrap blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks (  ) each to make a code block as demonstrated here.

Picard 2.10.4 has MAJOR CHANGES that impact throughput of pipelines. Default compression is now 1 instead of 5, and Picard now handles compressed data with the Intel Deflator/Inflator instead of JDK.
GATK version 4.beta.2 (i.e. the second beta release) is out. See the GATK4 BETA page for download and details.

# PhasebyTransmission error concerning Genotype Likelihood score

Member
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

Tagged:

Hi there,

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

• Member

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.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:268) at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:256)

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

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

• Member
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.

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...

• Member

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

Best!