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Wrong number of fields in PED files in PhaseByTransmission

Posts: 5Member
edited January 2013

Hello,all

while using the walker PhaseByTransmission I always get this error:

##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.1-12-ga99c19d):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR
##### ERROR MESSAGE: File associated with name java.io.FileReader@5cf7c5b5 is malformed: Bad PED line 1: wrong number of fields
##### ERROR ------------------------------------------------------------------------------------------


my conmmand is :

java -jar GenomeAnalysisTK-2.1-12-ga99c19d/GenomeAnalysisTK.jar -T  PhaseByTransmission -R GRCh37.fasta -V trios_457.chr22.vcf -ped trios_457.chr22.ped -pedValidationType SILENT -o o1.vcf


and my ped file is like this:

fam1    s_4     0       0       1       1       C       C       C       C       G       G
fam1    s_5     0       0       2       2       T       T       T       T       G       G
fam1    s_7     s_4     s_5     2       2       C       T       C       T       G       G


I do counted my vcf ped and map files and the result is:

-bash-4.1$head -1 trios_457.chr22.ped |wc -w 1892 #( 6 columns for info + 943*2 columns for alleles ) -bash-4.1$ wc -l trios_457.chr22.map
943

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

Thanks!

Thanks for reporting your solution; I'll update the documentation accordingly.

Geraldine Van der Auwera, PhD

• SouthKoreaPosts: 2Member

Hi to all

I got the same error msg. But i tried with the above solutions. But i am getting error msg.

same as like above, i created the ped file with VCFtools and i used the same

Still the error status is same..

Is there any alternative solutions ....

Hi Murthi,

Geraldine Van der Auwera, PhD

• SouthKoreaPosts: 2Member
edited September 2013

M41 G6 0 0 1 1 Korean
M41 G5 0 0 2 1 Korean
M41 G4 G6 G5 1 2 Korean

The file created by VCFtools

G4.variant G4.variant 0 0 0 0 0 0 G A C T A G A G 0 0......
G5.variant2 G5.variant2 0 0 0 0 0 0 0 0 C T 0 0 0 0 AC A ......
G6.variant3 G6.variant3 0 0 0 0 C C 0 0 C T 0 0 A G 0 0........

Post edited by Geraldine_VdAuwera on