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VariantsToBinaryPed

edited July 2012

A new tool has been released!

Check out the documentation at VariantsToBinaryPed.

Tagged:

• Posts: 5Member

I have had trouble getting the VariantsToBinaryPed tool to work. Below is the error I have been getting. I am using a .vcf file produced by the UnifiedGenotyper and selected down to those variants present in one of the 11 people in the test file I am using (used SelectVariants to subset). I used VariantValidator to check the test file and there were no errors.

WARN 14:41:13,090 VCFStandardHeaderLines\$Standards - Repairing standard header line for field AF because -- count types disagree; header has UNBOUNDED but standard is A
INFO 14:41:13,808 GATKRunReport - Uploaded run statistics report to AWS S3

ERROR stack trace

java.lang.ArrayIndexOutOfBoundsException: 1

ERROR ------------------------------------------------------------------------------------------

Also, can you post an example metaData file? I have tried reformating my .fam file a number of ways to see if that is a problem and haven't been to overcome this array out of bounds error.

Thank you

• Posts: 11Member

Any chance you can put an example of the metaData file up on the web? I am getting the same error message that another person commented about that there is no metaData for my subjects. I tried to run the VariantsToBinaryPed on a single subject, but I'm still having problems. I thought it could be my input metaData file, but I'm not sure if I have that wrong. Thanks!

• Posts: 6Member

Has anyone had any success with this tool?
Please show how you run it and how the .fam file should look!

Thank you

We have expanded the technical documentation on this tool; it will be available later today when we release version 2.2.

Geraldine Van der Auwera, PhD

• HoustonPosts: 3Member

@Geraldine_VdAuwera said:
We have expanded the technical documentation on this tool; it will be available later today when we release version 2.2.

Dear Geraldine, where can I find the documentation? Same problem. Thank you!

• HoustonPosts: 3Member

My Error Message:

ERROR stack trace

java.lang.ArrayIndexOutOfBoundsException: 1

ERROR ------------------------------------------------------------------------------------------

@Geraldine_VdAuwera said:
We have expanded the technical documentation on this tool; it will be available later today when we release version 2.2.

Thanks!

@dakezhang
Hi,

Can you post the exact command line you used?

Thanks,
Sheila

• HoustonPosts: 3Member

Hi Sheila, thks, as follows:

java -jar /Users/dakez/GenomeAnalysisTK-3.3-0/GenomeAnalysisTK.jar \
-R /Users/dakez/Homo_sapiens_assembly19.fasta \
-T VariantsToBinaryPed \
-V /Users/dakez/target.regions.full.vcf \
-m /Users/dakez/fam4.fam.txt \
-bed /Users/dakez/target.regions.full.bed \
-bim /Users/dakez/target.regions.full.bim \
-fam /Users/dakez/target.regions.full.fam \
-mgq 0 \



@Sheila said:
dakezhang
Hi,
Can you post the exact command line you used?
Thanks,
Sheila

Geraldine Van der Auwera, PhD