Wrong number of fields in PED files in PhaseByTransmission
Posted in Ask the team | Last updated on 2013-01-04 03:08:48


Comments (11)

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 Visit our website and forum for extensive documentation and answers to 
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### 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 
-bash-4.1$ grep -v "#" trios_457.chr22.vcf | wc -l
943

My question is what's wrong with my my PED line?


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